Starting phenix.real_space_refine on Fri Aug 7 10:31:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wv5_66282/08_2026/9wv5_66282.map" } resolution = 3.16 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= 0.001 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 13308 2.51 5 N 3416 2.21 5 O 3644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20492 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5123 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5123 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5123 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5123 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.95, per 1000 atoms: 0.19 Number of scatterers: 20492 At special positions: 0 Unit cell: (159.305, 159.305, 127.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3644 8.00 N 3416 7.00 C 13308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 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: 1.77 Conformation dependent library (CDL) restraints added in 825.1 milliseconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 66.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 131 through 147 removed outlier: 3.752A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.086A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.502A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.614A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 483 through 508 removed outlier: 3.732A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.625A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.933A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.712A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.739A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.640A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.755A pdb=" N ARG A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.701A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.087A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.618A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 508 removed outlier: 3.733A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.625A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.916A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.710A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.738A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 4.156A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.605A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.780A pdb=" N ARG B 714 " --> pdb=" O TRP B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.745A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.087A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.511A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 316 through 329 Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.615A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 483 through 508 removed outlier: 3.731A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.625A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.918A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.712A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.737A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 4.161A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.620A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.801A pdb=" N ARG C 714 " --> pdb=" O TRP C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 131 through 147 removed outlier: 3.701A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 4.087A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 316 through 329 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.613A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 483 through 508 removed outlier: 3.729A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 515 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.626A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.915A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.711A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.584A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 4.163A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.613A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.796A pdb=" N ARG D 714 " --> pdb=" O TRP D 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.946A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.944A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.945A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3486 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: 3.60 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6516 1.34 - 1.46: 4748 1.46 - 1.58: 9456 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 20924 Sorted by residual: bond pdb=" CA GLU A 687 " pdb=" CB GLU A 687 " ideal model delta sigma weight residual 1.535 1.548 -0.013 1.64e-02 3.72e+03 6.26e-01 bond pdb=" CB VAL A 140 " pdb=" CG1 VAL A 140 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.06e-01 bond pdb=" CB GLU A 687 " pdb=" CG GLU A 687 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 bond pdb=" CB VAL C 140 " pdb=" CG1 VAL C 140 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.92e-01 bond pdb=" CB GLU A 709 " pdb=" CG GLU A 709 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.36e-01 ... (remaining 20919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28079 1.74 - 3.48: 174 3.48 - 5.21: 18 5.21 - 6.95: 5 6.95 - 8.69: 4 Bond angle restraints: 28280 Sorted by residual: angle pdb=" CA LEU B 370 " pdb=" CB LEU B 370 " pdb=" CG LEU B 370 " ideal model delta sigma weight residual 116.30 124.99 -8.69 3.50e+00 8.16e-02 6.17e+00 angle pdb=" CA LEU A 370 " pdb=" CB LEU A 370 " pdb=" CG LEU A 370 " ideal model delta sigma weight residual 116.30 124.97 -8.67 3.50e+00 8.16e-02 6.13e+00 angle pdb=" CA LEU C 370 " pdb=" CB LEU C 370 " pdb=" CG LEU C 370 " ideal model delta sigma weight residual 116.30 124.94 -8.64 3.50e+00 8.16e-02 6.09e+00 angle pdb=" CA LEU D 370 " pdb=" CB LEU D 370 " pdb=" CG LEU D 370 " ideal model delta sigma weight residual 116.30 124.93 -8.63 3.50e+00 8.16e-02 6.08e+00 angle pdb=" C LYS C 435 " pdb=" N PHE C 436 " pdb=" CA PHE C 436 " ideal model delta sigma weight residual 121.54 118.00 3.54 1.91e+00 2.74e-01 3.43e+00 ... (remaining 28275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 11000 16.06 - 32.12: 1165 32.12 - 48.18: 269 48.18 - 64.24: 85 64.24 - 80.30: 13 Dihedral angle restraints: 12532 sinusoidal: 5120 harmonic: 7412 Sorted by residual: dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual 93.00 58.61 34.39 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB CYS D 721 " pdb=" SG CYS D 721 " pdb=" SG CYS D 731 " pdb=" CB CYS D 731 " ideal model delta sinusoidal sigma weight residual 93.00 58.63 34.37 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB CYS B 721 " pdb=" SG CYS B 721 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual 93.00 58.65 34.35 1 1.00e+01 1.00e-02 1.67e+01 ... (remaining 12529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2003 0.025 - 0.049: 753 0.049 - 0.074: 332 0.074 - 0.098: 98 0.098 - 0.123: 34 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA GLU C 137 " pdb=" N GLU C 137 " pdb=" C GLU C 137 " pdb=" CB GLU C 137 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 3217 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 710 " -0.010 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" CG TRP C 710 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 710 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 710 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 710 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 710 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 710 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 710 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 710 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 710 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 710 " 0.009 2.00e-02 2.50e+03 8.76e-03 1.92e+00 pdb=" CG TRP B 710 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 710 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 710 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 710 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 710 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 710 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 710 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 710 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 710 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 710 " -0.009 2.00e-02 2.50e+03 8.40e-03 1.76e+00 pdb=" CG TRP D 710 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP D 710 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 710 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 710 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 710 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 710 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 710 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 710 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 710 " -0.000 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4461 2.78 - 3.31: 20087 3.31 - 3.84: 33972 3.84 - 4.37: 39993 4.37 - 4.90: 69996 Nonbonded interactions: 168509 Sorted by model distance: nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.258 3.040 nonbonded pdb=" O ARG D 363 " pdb=" OG SER D 374 " model vdw 2.268 3.040 ... (remaining 168504 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.490 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.002 0.026 20928 Z= 0.080 Angle : 0.395 8.692 28288 Z= 0.205 Chirality : 0.033 0.123 3220 Planarity : 0.002 0.026 3532 Dihedral : 14.593 80.296 7704 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.21 (0.17), residues: 2492 helix: 1.64 (0.13), residues: 1612 sheet: 1.04 (0.58), residues: 84 loop : -0.98 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.008 0.001 TYR A 451 PHE 0.016 0.001 PHE A 445 TRP 0.028 0.001 TRP C 710 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.08 (20924) covalent geometry : angle 0.39458 / 0.20 (28280) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.56277 / 0.33 ( 8) hydrogen bonds : bond 0.18343 / 12.17 ( 1174) hydrogen bonds : angle 5.45064 / 3.91 ( 3486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.781 Fit side-chains REVERT: A 687 GLU cc_start: 0.7136 (pp20) cc_final: 0.6444 (pt0) REVERT: B 322 ASP cc_start: 0.8355 (t0) cc_final: 0.8124 (t0) REVERT: B 586 ASP cc_start: 0.7656 (m-30) cc_final: 0.7280 (m-30) REVERT: D 687 GLU cc_start: 0.7503 (pt0) cc_final: 0.7030 (pp20) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1493 time to fit residues: 82.1671 Evaluate side-chains 271 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 314 ASN A 417 HIS A 523 HIS B 197 ASN B 314 ASN C 197 ASN C 314 ASN C 570 GLN D 197 ASN D 314 ASN D 417 HIS D 570 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124405 restraints weight = 24431.407| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.97 r_work: 0.3318 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20928 Z= 0.184 Angle : 0.512 9.214 28288 Z= 0.267 Chirality : 0.038 0.133 3220 Planarity : 0.004 0.037 3532 Dihedral : 3.472 14.377 2740 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.08 % Allowed : 8.08 % Favored : 90.84 % 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: 1.28 (0.17), residues: 2492 helix: 1.74 (0.12), residues: 1632 sheet: 0.52 (0.54), residues: 84 loop : -1.04 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.014 0.002 TYR C 451 PHE 0.013 0.001 PHE C 522 TRP 0.018 0.001 TRP C 710 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (20924) covalent geometry : angle 0.51086 / 0.27 (28280) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 2.10566 / 1.22 ( 8) hydrogen bonds : bond 0.04441 / 3.02 ( 1174) hydrogen bonds : angle 4.23153 / 3.02 ( 3486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.800 Fit side-chains REVERT: A 647 ASN cc_start: 0.8223 (t0) cc_final: 0.7605 (t0) REVERT: A 663 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 322 ASP cc_start: 0.8583 (t0) cc_final: 0.8329 (t0) REVERT: B 524 PHE cc_start: 0.8110 (m-80) cc_final: 0.7874 (m-10) REVERT: B 586 ASP cc_start: 0.7827 (m-30) cc_final: 0.7420 (m-30) REVERT: B 647 ASN cc_start: 0.8190 (t0) cc_final: 0.7567 (t0) REVERT: B 663 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8374 (mp) REVERT: C 322 ASP cc_start: 0.8611 (t0) cc_final: 0.8372 (t0) REVERT: C 524 PHE cc_start: 0.8082 (m-80) cc_final: 0.7817 (m-10) REVERT: C 647 ASN cc_start: 0.8218 (t0) cc_final: 0.7597 (t0) REVERT: C 663 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8370 (mp) REVERT: D 647 ASN cc_start: 0.8203 (t0) cc_final: 0.7583 (t0) REVERT: D 663 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8367 (mp) outliers start: 24 outliers final: 9 residues processed: 323 average time/residue: 0.1591 time to fit residues: 79.2211 Evaluate side-chains 302 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 289 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 175 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 179 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS A 523 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 523 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.170934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134583 restraints weight = 24362.840| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.07 r_work: 0.3330 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20928 Z= 0.183 Angle : 0.496 8.612 28288 Z= 0.259 Chirality : 0.038 0.131 3220 Planarity : 0.004 0.044 3532 Dihedral : 3.711 14.334 2740 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.42 % Allowed : 10.01 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.23 (0.16), residues: 2492 helix: 1.70 (0.12), residues: 1608 sheet: 0.02 (0.54), residues: 84 loop : -0.92 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.015 0.002 TYR A 208 PHE 0.014 0.001 PHE A 522 TRP 0.019 0.002 TRP C 710 HIS 0.011 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (20924) covalent geometry : angle 0.49507 / 0.26 (28280) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 2.21224 / 1.28 ( 8) hydrogen bonds : bond 0.04216 / 2.85 ( 1174) hydrogen bonds : angle 4.12159 / 2.94 ( 3486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.765 Fit side-chains REVERT: A 322 ASP cc_start: 0.8701 (t0) cc_final: 0.8452 (t0) REVERT: A 430 HIS cc_start: 0.7839 (t-90) cc_final: 0.7190 (m170) REVERT: A 647 ASN cc_start: 0.8268 (t0) cc_final: 0.7699 (t0) REVERT: A 663 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 705 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8208 (mttt) REVERT: B 322 ASP cc_start: 0.8677 (t0) cc_final: 0.8422 (t0) REVERT: B 419 MET cc_start: 0.9111 (ptm) cc_final: 0.8864 (ttp) REVERT: B 430 HIS cc_start: 0.7827 (t-90) cc_final: 0.7156 (m170) REVERT: B 586 ASP cc_start: 0.7783 (m-30) cc_final: 0.7502 (m-30) REVERT: B 647 ASN cc_start: 0.8254 (t0) cc_final: 0.7683 (t0) REVERT: B 663 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 705 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8290 (mtmm) REVERT: B 717 MET cc_start: 0.8898 (mmp) cc_final: 0.8696 (mmt) REVERT: C 322 ASP cc_start: 0.8717 (t0) cc_final: 0.8473 (t0) REVERT: C 419 MET cc_start: 0.9095 (ptm) cc_final: 0.8840 (ttp) REVERT: C 647 ASN cc_start: 0.8264 (t0) cc_final: 0.7691 (t0) REVERT: C 663 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 705 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: D 322 ASP cc_start: 0.8703 (t0) cc_final: 0.8453 (t0) REVERT: D 647 ASN cc_start: 0.8242 (t0) cc_final: 0.7656 (t0) REVERT: D 663 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 705 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8304 (mtmm) outliers start: 54 outliers final: 18 residues processed: 332 average time/residue: 0.1549 time to fit residues: 79.9483 Evaluate side-chains 320 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 705 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 705 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 203 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 236 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.158916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121163 restraints weight = 24610.720| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.07 r_work: 0.3349 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20928 Z= 0.143 Angle : 0.459 8.081 28288 Z= 0.241 Chirality : 0.036 0.130 3220 Planarity : 0.003 0.043 3532 Dihedral : 3.617 13.632 2740 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.06 % Allowed : 10.73 % Favored : 87.21 % 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: 1.31 (0.17), residues: 2492 helix: 1.80 (0.12), residues: 1612 sheet: -0.12 (0.53), residues: 84 loop : -0.95 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 369 TYR 0.012 0.002 TYR D 208 PHE 0.011 0.001 PHE B 316 TRP 0.017 0.001 TRP D 710 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (20924) covalent geometry : angle 0.45781 / 0.24 (28280) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 1.76510 / 1.01 ( 8) hydrogen bonds : bond 0.03812 / 2.57 ( 1174) hydrogen bonds : angle 3.95484 / 2.82 ( 3486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 0.828 Fit side-chains REVERT: A 322 ASP cc_start: 0.8697 (t0) cc_final: 0.8442 (t0) REVERT: A 430 HIS cc_start: 0.7933 (t-90) cc_final: 0.7165 (m170) REVERT: A 647 ASN cc_start: 0.8270 (t0) cc_final: 0.7694 (t0) REVERT: A 663 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 705 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8187 (mttt) REVERT: B 322 ASP cc_start: 0.8676 (t0) cc_final: 0.8403 (t0) REVERT: B 430 HIS cc_start: 0.7926 (t-90) cc_final: 0.7161 (m170) REVERT: B 647 ASN cc_start: 0.8258 (t0) cc_final: 0.7735 (t0) REVERT: B 663 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 322 ASP cc_start: 0.8689 (t0) cc_final: 0.8439 (t0) REVERT: C 647 ASN cc_start: 0.8258 (t0) cc_final: 0.7678 (t0) REVERT: C 663 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8326 (mp) REVERT: D 322 ASP cc_start: 0.8685 (t0) cc_final: 0.8427 (t0) REVERT: D 663 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8315 (mp) outliers start: 46 outliers final: 22 residues processed: 327 average time/residue: 0.1560 time to fit residues: 79.6189 Evaluate side-chains 312 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 181 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120549 restraints weight = 24453.248| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.98 r_work: 0.3381 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20928 Z= 0.174 Angle : 0.480 8.136 28288 Z= 0.251 Chirality : 0.037 0.129 3220 Planarity : 0.004 0.042 3532 Dihedral : 3.691 14.369 2740 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.28 % Allowed : 10.68 % Favored : 86.04 % 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: 1.24 (0.17), residues: 2492 helix: 1.75 (0.12), residues: 1608 sheet: -0.30 (0.53), residues: 84 loop : -0.96 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.014 0.002 TYR C 208 PHE 0.012 0.001 PHE D 522 TRP 0.019 0.002 TRP C 710 HIS 0.008 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (20924) covalent geometry : angle 0.47851 / 0.25 (28280) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 2.00874 / 1.15 ( 8) hydrogen bonds : bond 0.03905 / 2.63 ( 1174) hydrogen bonds : angle 3.98306 / 2.84 ( 3486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 297 time to evaluate : 0.787 Fit side-chains REVERT: A 322 ASP cc_start: 0.8468 (t0) cc_final: 0.8189 (t0) REVERT: A 419 MET cc_start: 0.9122 (ptm) cc_final: 0.8909 (ttp) REVERT: A 430 HIS cc_start: 0.7619 (t-90) cc_final: 0.6932 (m170) REVERT: A 647 ASN cc_start: 0.8139 (t0) cc_final: 0.7570 (t0) REVERT: A 663 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 705 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8137 (mttt) REVERT: B 322 ASP cc_start: 0.8432 (t0) cc_final: 0.8134 (t0) REVERT: B 419 MET cc_start: 0.9102 (ptm) cc_final: 0.8869 (ttp) REVERT: B 430 HIS cc_start: 0.7655 (t-90) cc_final: 0.6970 (m170) REVERT: B 647 ASN cc_start: 0.8129 (t0) cc_final: 0.7561 (t0) REVERT: B 663 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 134 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5892 (pm20) REVERT: C 322 ASP cc_start: 0.8476 (t0) cc_final: 0.8192 (t0) REVERT: C 419 MET cc_start: 0.9109 (ptm) cc_final: 0.8863 (ttp) REVERT: C 647 ASN cc_start: 0.8136 (t0) cc_final: 0.7567 (t0) REVERT: C 663 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8276 (mp) REVERT: D 322 ASP cc_start: 0.8465 (t0) cc_final: 0.8180 (t0) REVERT: D 647 ASN cc_start: 0.8126 (t0) cc_final: 0.7552 (t0) REVERT: D 663 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8266 (mp) outliers start: 73 outliers final: 38 residues processed: 347 average time/residue: 0.1542 time to fit residues: 83.5721 Evaluate side-chains 335 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN B 313 GLN C 313 GLN D 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121955 restraints weight = 24344.862| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.01 r_work: 0.3382 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20928 Z= 0.145 Angle : 0.457 7.751 28288 Z= 0.240 Chirality : 0.036 0.137 3220 Planarity : 0.003 0.042 3532 Dihedral : 3.629 14.048 2740 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.32 % Allowed : 10.77 % Favored : 85.91 % 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: 1.33 (0.17), residues: 2492 helix: 1.83 (0.13), residues: 1608 sheet: -0.35 (0.52), residues: 84 loop : -0.95 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.012 0.002 TYR A 208 PHE 0.012 0.001 PHE A 445 TRP 0.025 0.002 TRP C 710 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (20924) covalent geometry : angle 0.45660 / 0.24 (28280) SS BOND : bond 0.00111 / 0.06 ( 4) SS BOND : angle 1.70711 / 0.98 ( 8) hydrogen bonds : bond 0.03726 / 2.51 ( 1174) hydrogen bonds : angle 3.89689 / 2.78 ( 3486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 0.986 Fit side-chains REVERT: A 322 ASP cc_start: 0.8559 (t0) cc_final: 0.8306 (t0) REVERT: A 419 MET cc_start: 0.9078 (ptm) cc_final: 0.8832 (ttp) REVERT: A 430 HIS cc_start: 0.7787 (t-90) cc_final: 0.7140 (m170) REVERT: A 647 ASN cc_start: 0.8202 (t0) cc_final: 0.7688 (t0) REVERT: A 663 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 705 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8221 (mttt) REVERT: B 322 ASP cc_start: 0.8528 (t0) cc_final: 0.8249 (t0) REVERT: B 419 MET cc_start: 0.9017 (ptm) cc_final: 0.8800 (ttp) REVERT: B 430 HIS cc_start: 0.7796 (t-90) cc_final: 0.7134 (m170) REVERT: B 663 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 322 ASP cc_start: 0.8579 (t0) cc_final: 0.8324 (t0) REVERT: C 419 MET cc_start: 0.9019 (ptm) cc_final: 0.8779 (ttp) REVERT: C 647 ASN cc_start: 0.8197 (t0) cc_final: 0.7678 (t0) REVERT: C 663 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8399 (mp) REVERT: D 322 ASP cc_start: 0.8556 (t0) cc_final: 0.8295 (t0) REVERT: D 647 ASN cc_start: 0.8189 (t0) cc_final: 0.7670 (t0) REVERT: D 663 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8381 (mp) outliers start: 74 outliers final: 45 residues processed: 355 average time/residue: 0.1576 time to fit residues: 86.1935 Evaluate side-chains 343 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 672 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 191 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 211 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN C 314 ASN D 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.160688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125372 restraints weight = 24522.857| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.95 r_work: 0.3478 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20928 Z= 0.101 Angle : 0.429 7.384 28288 Z= 0.227 Chirality : 0.034 0.150 3220 Planarity : 0.003 0.038 3532 Dihedral : 3.446 12.330 2740 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 12.75 % Favored : 85.32 % 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: 1.61 (0.17), residues: 2492 helix: 2.05 (0.13), residues: 1612 sheet: -0.26 (0.52), residues: 84 loop : -0.86 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 202 TYR 0.010 0.001 TYR B 451 PHE 0.012 0.001 PHE B 316 TRP 0.029 0.002 TRP C 710 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20924) covalent geometry : angle 0.42907 / 0.23 (28280) SS BOND : bond 0.00257 / 0.13 ( 4) SS BOND : angle 1.09344 / 0.63 ( 8) hydrogen bonds : bond 0.03383 / 2.27 ( 1174) hydrogen bonds : angle 3.73973 / 2.67 ( 3486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.778 Fit side-chains REVERT: A 419 MET cc_start: 0.9024 (ptm) cc_final: 0.8798 (ttp) REVERT: A 430 HIS cc_start: 0.7563 (t-90) cc_final: 0.6990 (m170) REVERT: A 632 LEU cc_start: 0.8848 (mp) cc_final: 0.8643 (mp) REVERT: A 647 ASN cc_start: 0.8167 (t0) cc_final: 0.7655 (t0) REVERT: A 663 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 705 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8133 (mttt) REVERT: B 322 ASP cc_start: 0.8301 (t0) cc_final: 0.8003 (t0) REVERT: B 430 HIS cc_start: 0.7568 (t-90) cc_final: 0.6979 (m170) REVERT: B 632 LEU cc_start: 0.8850 (mp) cc_final: 0.8644 (mp) REVERT: B 647 ASN cc_start: 0.8157 (t0) cc_final: 0.7641 (t0) REVERT: B 663 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 632 LEU cc_start: 0.8851 (mp) cc_final: 0.8643 (mp) REVERT: C 663 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8303 (mp) REVERT: D 580 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6874 (mm-40) REVERT: D 647 ASN cc_start: 0.8159 (t0) cc_final: 0.7638 (t0) REVERT: D 663 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8282 (mp) outliers start: 43 outliers final: 32 residues processed: 341 average time/residue: 0.1587 time to fit residues: 83.9724 Evaluate side-chains 335 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 706 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 15 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.159010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124931 restraints weight = 24446.708| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.90 r_work: 0.3439 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20928 Z= 0.133 Angle : 0.462 9.768 28288 Z= 0.239 Chirality : 0.035 0.146 3220 Planarity : 0.003 0.038 3532 Dihedral : 3.498 12.929 2740 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.24 % Allowed : 12.84 % Favored : 84.92 % 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: 1.52 (0.17), residues: 2492 helix: 1.98 (0.13), residues: 1612 sheet: -0.38 (0.52), residues: 84 loop : -0.88 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 202 TYR 0.011 0.002 TYR B 451 PHE 0.013 0.001 PHE A 445 TRP 0.034 0.002 TRP C 710 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (20924) covalent geometry : angle 0.46091 / 0.24 (28280) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 1.50753 / 0.87 ( 8) hydrogen bonds : bond 0.03563 / 2.40 ( 1174) hydrogen bonds : angle 3.79102 / 2.71 ( 3486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 0.777 Fit side-chains REVERT: A 322 ASP cc_start: 0.8410 (t0) cc_final: 0.8138 (t0) REVERT: A 430 HIS cc_start: 0.7634 (t-90) cc_final: 0.7053 (m170) REVERT: A 647 ASN cc_start: 0.8181 (t0) cc_final: 0.7664 (t0) REVERT: A 663 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 705 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8114 (mttt) REVERT: B 322 ASP cc_start: 0.8370 (t0) cc_final: 0.8076 (t0) REVERT: B 647 ASN cc_start: 0.8169 (t0) cc_final: 0.7651 (t0) REVERT: B 663 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 647 ASN cc_start: 0.8180 (t0) cc_final: 0.7661 (t0) REVERT: C 663 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 580 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6909 (mm-40) REVERT: D 647 ASN cc_start: 0.8166 (t0) cc_final: 0.7650 (t0) REVERT: D 663 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 50 outliers final: 37 residues processed: 333 average time/residue: 0.1565 time to fit residues: 81.2409 Evaluate side-chains 344 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 706 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 39 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 179 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122015 restraints weight = 24270.072| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.99 r_work: 0.3395 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20928 Z= 0.112 Angle : 0.455 9.495 28288 Z= 0.236 Chirality : 0.035 0.153 3220 Planarity : 0.003 0.037 3532 Dihedral : 3.443 16.162 2740 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.93 % Allowed : 13.51 % Favored : 84.56 % 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: 1.55 (0.17), residues: 2492 helix: 2.03 (0.13), residues: 1620 sheet: -0.34 (0.52), residues: 84 loop : -0.97 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.011 0.001 TYR B 451 PHE 0.012 0.001 PHE B 316 TRP 0.039 0.002 TRP C 710 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20924) covalent geometry : angle 0.45430 / 0.24 (28280) SS BOND : bond 0.00144 / 0.07 ( 4) SS BOND : angle 1.20332 / 0.70 ( 8) hydrogen bonds : bond 0.03398 / 2.29 ( 1174) hydrogen bonds : angle 3.74141 / 2.67 ( 3486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.856 Fit side-chains REVERT: A 322 ASP cc_start: 0.8316 (t0) cc_final: 0.8028 (t0) REVERT: A 632 LEU cc_start: 0.8748 (mp) cc_final: 0.8543 (mp) REVERT: A 647 ASN cc_start: 0.8115 (t0) cc_final: 0.7543 (t0) REVERT: A 663 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 705 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8035 (mttt) REVERT: B 322 ASP cc_start: 0.8280 (t0) cc_final: 0.7954 (t0) REVERT: B 647 ASN cc_start: 0.8107 (t0) cc_final: 0.7530 (t0) REVERT: B 663 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 253 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7700 (mmmm) REVERT: C 632 LEU cc_start: 0.8759 (mp) cc_final: 0.8551 (mp) REVERT: C 647 ASN cc_start: 0.8108 (t0) cc_final: 0.7530 (t0) REVERT: C 663 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 431 MET cc_start: 0.7680 (mtm) cc_final: 0.7466 (ptm) REVERT: D 580 GLN cc_start: 0.7018 (mm-40) cc_final: 0.6707 (mm-40) REVERT: D 647 ASN cc_start: 0.8090 (t0) cc_final: 0.7527 (t0) REVERT: D 663 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8210 (mp) outliers start: 43 outliers final: 37 residues processed: 342 average time/residue: 0.1558 time to fit residues: 82.7694 Evaluate side-chains 352 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 706 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 113 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.158746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123124 restraints weight = 24391.014| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.90 r_work: 0.3334 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20928 Z= 0.146 Angle : 0.485 9.804 28288 Z= 0.250 Chirality : 0.036 0.238 3220 Planarity : 0.003 0.037 3532 Dihedral : 3.528 13.117 2740 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 13.29 % Favored : 84.74 % 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: 1.38 (0.17), residues: 2492 helix: 1.90 (0.13), residues: 1616 sheet: -0.50 (0.51), residues: 84 loop : -1.01 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 202 TYR 0.012 0.002 TYR D 208 PHE 0.014 0.001 PHE C 445 TRP 0.051 0.002 TRP C 710 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (20924) covalent geometry : angle 0.48458 / 0.25 (28280) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 1.60965 / 0.92 ( 8) hydrogen bonds : bond 0.03618 / 2.43 ( 1174) hydrogen bonds : angle 3.81817 / 2.72 ( 3486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 0.831 Fit side-chains REVERT: A 647 ASN cc_start: 0.8308 (t0) cc_final: 0.7795 (t0) REVERT: A 663 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 705 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: B 322 ASP cc_start: 0.8641 (t0) cc_final: 0.8373 (t0) REVERT: B 647 ASN cc_start: 0.8254 (t0) cc_final: 0.7732 (t0) REVERT: B 663 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8375 (mp) REVERT: C 147 ARG cc_start: 0.7278 (mmt-90) cc_final: 0.6986 (mmt-90) REVERT: C 647 ASN cc_start: 0.8298 (t0) cc_final: 0.7785 (t0) REVERT: C 663 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 580 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7000 (mm-40) REVERT: D 647 ASN cc_start: 0.8247 (t0) cc_final: 0.7726 (t0) REVERT: D 649 LYS cc_start: 0.7755 (tptp) cc_final: 0.7479 (tptt) REVERT: D 663 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8383 (mp) outliers start: 44 outliers final: 39 residues processed: 339 average time/residue: 0.1586 time to fit residues: 83.5428 Evaluate side-chains 353 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 706 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 174 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 187 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.163270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128580 restraints weight = 24214.069| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3205 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20928 Z= 0.101 Angle : 0.458 9.367 28288 Z= 0.236 Chirality : 0.035 0.184 3220 Planarity : 0.003 0.036 3532 Dihedral : 3.410 13.066 2740 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.93 % Allowed : 13.73 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.17), residues: 2492 helix: 2.03 (0.13), residues: 1620 sheet: -0.44 (0.51), residues: 84 loop : -0.96 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.010 0.001 TYR A 451 PHE 0.011 0.001 PHE B 316 TRP 0.052 0.002 TRP C 710 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (20924) covalent geometry : angle 0.45794 / 0.24 (28280) SS BOND : bond 0.00225 / 0.11 ( 4) SS BOND : angle 1.04560 / 0.61 ( 8) hydrogen bonds : bond 0.03316 / 2.23 ( 1174) hydrogen bonds : angle 3.73008 / 2.66 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.87 seconds wall clock time: 89 minutes 58.54 seconds (5398.54 seconds total)