Starting phenix.real_space_refine on Tue Feb 3 21:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps6_71824/02_2026/9ps6_71824.map" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.016 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: 3 Type Number sf(0) Gaussians C 4254 2.51 5 N 1455 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7164 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 2388 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1463 Unresolved non-hydrogen angles: 1926 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'ARG:plan': 19, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 35, 'HIS:plan': 5, 'GLU:plan': 8, 'TYR:plan': 17, 'TRP:plan': 10, 'GLN:plan1': 11} Unresolved non-hydrogen planarities: 705 Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 2388 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1463 Unresolved non-hydrogen angles: 1926 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'ARG:plan': 19, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 35, 'HIS:plan': 5, 'GLU:plan': 8, 'TYR:plan': 17, 'TRP:plan': 10, 'GLN:plan1': 11} Unresolved non-hydrogen planarities: 705 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 2388 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 21, 'TRANS': 463} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1463 Unresolved non-hydrogen angles: 1926 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'ARG:plan': 19, 'ASN:plan1': 15, 'ASP:plan': 15, 'PHE:plan': 35, 'HIS:plan': 5, 'GLU:plan': 8, 'TYR:plan': 17, 'TRP:plan': 10, 'GLN:plan1': 11} Unresolved non-hydrogen planarities: 705 Time building chain proxies: 1.72, per 1000 atoms: 0.24 Number of scatterers: 7164 At special positions: 0 Unit cell: (129.86, 120.4, 79.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1455 8.00 N 1455 7.00 C 4254 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 - 3.00 Amino acid : True - 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: 0.64 Conformation dependent library (CDL) restraints added in 384.8 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 85.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 54 through 59 removed outlier: 4.164A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 121 removed outlier: 3.650A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 136 through 162 removed outlier: 4.358A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.547A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 254 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.910A pdb=" N THR B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 342 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.763A pdb=" N VAL B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 390 through 408 removed outlier: 4.356A pdb=" N ALA B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 451 removed outlier: 3.981A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 482 removed outlier: 4.178A pdb=" N ALA B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.572A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 4.162A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.970A pdb=" N CYS C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 121 removed outlier: 3.564A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.579A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 193 removed outlier: 3.501A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 removed outlier: 3.586A pdb=" N PHE C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 254 Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 313 through 320 Processing helix chain 'C' and resid 321 through 340 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.936A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.510A pdb=" N ILE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 382' Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 390 through 409 Processing helix chain 'C' and resid 417 through 452 removed outlier: 4.015A pdb=" N PHE C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 481 removed outlier: 3.500A pdb=" N LEU C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.516A pdb=" N ALA C 487 " --> pdb=" O TYR C 483 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 549 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 554 through 577 removed outlier: 3.881A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.971A pdb=" N CYS A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.564A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.501A pdb=" N ALA A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 removed outlier: 3.586A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 321 through 342 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.935A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.512A pdb=" N ILE A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 390 through 409 Processing helix chain 'A' and resid 417 through 452 removed outlier: 4.015A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 481 removed outlier: 3.500A pdb=" N LEU A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.516A pdb=" N ALA A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 577 removed outlier: 3.880A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.581A pdb=" N PHE B 195 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.673A pdb=" N LEU B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 196 removed outlier: 3.546A pdb=" N PHE C 195 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.547A pdb=" N PHE A 195 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 384 862 hydrogen bonds defined for protein. 2556 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: 0.84 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1455 1.28 - 1.35: 1444 1.35 - 1.42: 5 1.42 - 1.48: 1336 1.48 - 1.55: 2918 Bond restraints: 7158 Sorted by residual: bond pdb=" N VAL B 450 " pdb=" CA VAL B 450 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" CA ASN B 71 " pdb=" C ASN B 71 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.06e-02 8.90e+03 8.77e+00 bond pdb=" N VAL B 404 " pdb=" CA VAL B 404 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.14e-02 7.69e+03 8.72e+00 bond pdb=" N ILE A 322 " pdb=" CA ILE A 322 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.41e+00 bond pdb=" N ILE C 322 " pdb=" CA ILE C 322 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 ... (remaining 7153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9146 1.34 - 2.69: 671 2.69 - 4.03: 112 4.03 - 5.37: 13 5.37 - 6.72: 3 Bond angle restraints: 9945 Sorted by residual: angle pdb=" C PHE B 407 " pdb=" N ALA B 408 " pdb=" CA ALA B 408 " ideal model delta sigma weight residual 122.42 116.99 5.43 1.33e+00 5.65e-01 1.66e+01 angle pdb=" N GLY B 78 " pdb=" CA GLY B 78 " pdb=" C GLY B 78 " ideal model delta sigma weight residual 115.08 110.33 4.75 1.19e+00 7.06e-01 1.59e+01 angle pdb=" N VAL B 404 " pdb=" CA VAL B 404 " pdb=" C VAL B 404 " ideal model delta sigma weight residual 110.36 106.21 4.15 1.05e+00 9.07e-01 1.56e+01 angle pdb=" N CYS B 74 " pdb=" CA CYS B 74 " pdb=" C CYS B 74 " ideal model delta sigma weight residual 112.99 106.65 6.34 1.61e+00 3.86e-01 1.55e+01 angle pdb=" N LYS C 134 " pdb=" CA LYS C 134 " pdb=" C LYS C 134 " ideal model delta sigma weight residual 111.74 106.60 5.14 1.35e+00 5.49e-01 1.45e+01 ... (remaining 9940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.14: 3587 3.14 - 6.27: 423 6.27 - 9.41: 84 9.41 - 12.54: 38 12.54 - 15.68: 5 Dihedral angle restraints: 4137 sinusoidal: 0 harmonic: 4137 Sorted by residual: dihedral pdb=" CA THR B 143 " pdb=" C THR B 143 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA PHE C 426 " pdb=" C PHE C 426 " pdb=" N LEU C 427 " pdb=" CA LEU C 427 " ideal model delta harmonic sigma weight residual -180.00 -165.78 -14.22 0 5.00e+00 4.00e-02 8.09e+00 dihedral pdb=" CA PHE A 426 " pdb=" C PHE A 426 " pdb=" N LEU A 427 " pdb=" CA LEU A 427 " ideal model delta harmonic sigma weight residual -180.00 -165.81 -14.19 0 5.00e+00 4.00e-02 8.05e+00 ... (remaining 4134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 814 0.041 - 0.083: 369 0.083 - 0.124: 133 0.124 - 0.166: 6 0.166 - 0.207: 22 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA LEU C 537 " pdb=" N LEU C 537 " pdb=" C LEU C 537 " pdb=" CB LEU C 537 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE C 129 " pdb=" N ILE C 129 " pdb=" C ILE C 129 " pdb=" CB ILE C 129 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1341 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 69 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C LYS B 69 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 69 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG B 70 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 403 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C SER B 403 " 0.050 2.00e-02 2.50e+03 pdb=" O SER B 403 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 404 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 531 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C LEU A 531 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 531 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 532 " 0.010 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 4634 3.00 - 3.48: 8481 3.48 - 3.95: 9678 3.95 - 4.43: 10989 4.43 - 4.90: 15662 Nonbonded interactions: 49444 Sorted by model distance: nonbonded pdb=" O LEU B 95 " pdb=" C LEU B 96 " model vdw 2.527 3.270 nonbonded pdb=" N CYS B 74 " pdb=" N HIS B 75 " model vdw 2.549 2.560 nonbonded pdb=" O SER B 403 " pdb=" C VAL B 404 " model vdw 2.553 3.270 nonbonded pdb=" N PRO B 72 " pdb=" O PRO B 72 " model vdw 2.573 2.496 nonbonded pdb=" O VAL B 441 " pdb=" C ASN B 442 " model vdw 2.592 3.270 ... (remaining 49439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.006 0.036 7158 Z= 0.448 Angle : 0.765 6.715 9945 Z= 0.615 Chirality : 0.053 0.207 1344 Planarity : 0.004 0.034 1449 Dihedral : 3.730 15.679 1449 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1443 helix: 1.54 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 7158) covalent geometry : angle 0.76524 ( 9945) hydrogen bonds : bond 0.15514 ( 862) hydrogen bonds : angle 6.51875 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0250 time to fit residues: 0.6784 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055246 restraints weight = 57499.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055950 restraints weight = 48190.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056556 restraints weight = 41435.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056925 restraints weight = 36248.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057413 restraints weight = 32509.941| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7158 Z= 0.176 Angle : 0.431 4.953 9945 Z= 0.290 Chirality : 0.040 0.121 1344 Planarity : 0.003 0.028 1449 Dihedral : 3.654 18.471 1449 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.22), residues: 1443 helix: 2.84 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : 0.36 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7158) covalent geometry : angle 0.43055 ( 9945) hydrogen bonds : bond 0.04017 ( 862) hydrogen bonds : angle 3.91971 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0298 time to fit residues: 0.8643 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 95 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 124 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 3.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051329 restraints weight = 61448.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052083 restraints weight = 49989.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052685 restraints weight = 42182.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053178 restraints weight = 36757.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053523 restraints weight = 32622.026| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7158 Z= 0.150 Angle : 0.388 6.181 9945 Z= 0.257 Chirality : 0.040 0.119 1344 Planarity : 0.002 0.013 1449 Dihedral : 3.382 17.303 1449 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.27 (0.22), residues: 1443 helix: 3.40 (0.15), residues: 1147 sheet: None (None), residues: 0 loop : 0.31 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7158) covalent geometry : angle 0.38822 ( 9945) hydrogen bonds : bond 0.03766 ( 862) hydrogen bonds : angle 3.52437 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0293 time to fit residues: 0.8460 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 79 optimal weight: 40.0000 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047682 restraints weight = 65438.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048417 restraints weight = 50928.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048981 restraints weight = 41549.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049444 restraints weight = 35330.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049679 restraints weight = 30473.119| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7158 Z= 0.161 Angle : 0.388 5.713 9945 Z= 0.259 Chirality : 0.040 0.115 1344 Planarity : 0.002 0.016 1449 Dihedral : 3.549 18.621 1449 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.37 (0.22), residues: 1443 helix: 3.47 (0.15), residues: 1151 sheet: None (None), residues: 0 loop : 0.32 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7158) covalent geometry : angle 0.38757 ( 9945) hydrogen bonds : bond 0.03347 ( 862) hydrogen bonds : angle 3.48922 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0313 time to fit residues: 0.9214 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 118 optimal weight: 60.0000 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045464 restraints weight = 67928.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046126 restraints weight = 52060.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046693 restraints weight = 42619.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047141 restraints weight = 35618.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047486 restraints weight = 30878.967| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7158 Z= 0.198 Angle : 0.431 7.480 9945 Z= 0.287 Chirality : 0.040 0.118 1344 Planarity : 0.002 0.013 1449 Dihedral : 3.637 18.054 1449 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.22), residues: 1443 helix: 3.32 (0.14), residues: 1152 sheet: None (None), residues: 0 loop : 0.25 (0.41), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7158) covalent geometry : angle 0.43068 ( 9945) hydrogen bonds : bond 0.03819 ( 862) hydrogen bonds : angle 3.71840 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0313 time to fit residues: 0.8707 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.046457 restraints weight = 67485.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047193 restraints weight = 51694.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047765 restraints weight = 41675.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048204 restraints weight = 35073.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048512 restraints weight = 30383.899| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7158 Z= 0.114 Angle : 0.344 7.000 9945 Z= 0.222 Chirality : 0.039 0.116 1344 Planarity : 0.002 0.013 1449 Dihedral : 3.400 17.723 1449 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.77 (0.22), residues: 1443 helix: 3.78 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : 0.22 (0.41), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00151 ( 7158) covalent geometry : angle 0.34432 ( 9945) hydrogen bonds : bond 0.02964 ( 862) hydrogen bonds : angle 3.24348 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0311 time to fit residues: 0.9129 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.043875 restraints weight = 70477.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044557 restraints weight = 53672.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044937 restraints weight = 43326.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.045451 restraints weight = 36975.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.045756 restraints weight = 31731.578| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7158 Z= 0.308 Angle : 0.502 7.331 9945 Z= 0.357 Chirality : 0.041 0.124 1344 Planarity : 0.003 0.017 1449 Dihedral : 4.056 19.054 1449 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.22), residues: 1443 helix: 2.78 (0.14), residues: 1161 sheet: None (None), residues: 0 loop : 0.17 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7158) covalent geometry : angle 0.50161 ( 9945) hydrogen bonds : bond 0.04149 ( 862) hydrogen bonds : angle 4.28653 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0300 time to fit residues: 0.8549 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.044542 restraints weight = 70579.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.045228 restraints weight = 53294.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.045736 restraints weight = 42722.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.046142 restraints weight = 36052.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046477 restraints weight = 31239.429| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7158 Z= 0.233 Angle : 0.448 8.868 9945 Z= 0.305 Chirality : 0.040 0.117 1344 Planarity : 0.003 0.015 1449 Dihedral : 4.111 20.703 1449 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.22), residues: 1443 helix: 2.74 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.23 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7158) covalent geometry : angle 0.44829 ( 9945) hydrogen bonds : bond 0.03794 ( 862) hydrogen bonds : angle 4.16045 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0306 time to fit residues: 0.8918 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 79 optimal weight: 40.0000 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.0000 chunk 90 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045330 restraints weight = 69158.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045911 restraints weight = 52345.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046518 restraints weight = 43052.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.046892 restraints weight = 35923.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047261 restraints weight = 31320.897| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7158 Z= 0.160 Angle : 0.386 9.687 9945 Z= 0.254 Chirality : 0.040 0.121 1344 Planarity : 0.002 0.013 1449 Dihedral : 3.716 19.088 1449 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.22), residues: 1443 helix: 3.28 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7158) covalent geometry : angle 0.38618 ( 9945) hydrogen bonds : bond 0.03319 ( 862) hydrogen bonds : angle 3.68323 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0304 time to fit residues: 0.8592 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044674 restraints weight = 69685.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045357 restraints weight = 52761.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045898 restraints weight = 42467.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.046308 restraints weight = 35589.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046568 restraints weight = 30875.656| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7158 Z= 0.204 Angle : 0.422 8.492 9945 Z= 0.284 Chirality : 0.040 0.117 1344 Planarity : 0.002 0.014 1449 Dihedral : 3.854 19.732 1449 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.22), residues: 1443 helix: 3.10 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7158) covalent geometry : angle 0.42182 ( 9945) hydrogen bonds : bond 0.03634 ( 862) hydrogen bonds : angle 3.89764 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0264 time to fit residues: 0.8611 Evaluate side-chains 9 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 60.0000 chunk 126 optimal weight: 50.0000 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045424 restraints weight = 69199.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.046130 restraints weight = 52542.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046703 restraints weight = 42078.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.047098 restraints weight = 35196.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.047324 restraints weight = 30618.359| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7158 Z= 0.152 Angle : 0.374 8.951 9945 Z= 0.246 Chirality : 0.040 0.116 1344 Planarity : 0.002 0.012 1449 Dihedral : 3.621 18.871 1449 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.22), residues: 1443 helix: 3.46 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.29 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 80 PHE 0.000 0.000 PHE B 67 TRP 0.000 0.000 TRP B 106 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 7158) covalent geometry : angle 0.37372 ( 9945) hydrogen bonds : bond 0.03172 ( 862) hydrogen bonds : angle 3.56578 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 998.27 seconds wall clock time: 17 minutes 43.36 seconds (1063.36 seconds total)