Starting phenix.real_space_refine on Thu Mar 5 03:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.map" model { file = "/net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj0_33214/03_2026/7xj0_33214.cif" } resolution = 2.53 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= -0.000 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 12441 2.51 5 N 3069 2.21 5 O 3149 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18791 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4591 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 13, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 26, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4583 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 13, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 26, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4575 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 4 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 452 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 251 Chain: "D" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4572 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Unusual residues: {'6OU': 5, 'EQK': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'6OU:plan-2': 4, '6OU:plan-3': 5, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Unusual residues: {'6OU': 5, 'EQK': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'6OU:plan-3': 5, '6OU:plan-2': 4} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 131 Unusual residues: {'6OU': 6, 'EQK': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-2': 5, '6OU:plan-3': 6, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'6OU': 4, 'EQK': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 4.87, per 1000 atoms: 0.26 Number of scatterers: 18791 At special positions: 0 Unit cell: (127.92, 127.92, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 4 15.00 F 12 9.00 O 3149 8.00 N 3069 7.00 C 12441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.84 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: 1.67 Conformation dependent library (CDL) restraints added in 707.7 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 67.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.063A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.584A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.915A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 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 307 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.523A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 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 removed outlier: 4.467A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.801A 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 481 through 507 Processing helix chain 'B' and resid 520 through 542 Processing helix chain 'B' and resid 546 through 562 removed outlier: 3.536A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.559A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 608 Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 667 Processing helix chain 'B' and resid 668 through 685 Processing helix chain 'B' and resid 687 through 707 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 132 through 148 removed outlier: 4.064A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.584A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.914A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 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 307 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.522A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 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 removed outlier: 4.563A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.657A 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 481 through 507 Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 546 through 562 removed outlier: 3.513A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.559A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.647A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.590A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 667 Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 687 through 707 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 148 removed outlier: 4.064A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.584A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.914A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 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 307 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.522A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 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 removed outlier: 4.377A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.667A 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 481 through 507 Processing helix chain 'A' and resid 520 through 542 Processing helix chain 'A' and resid 546 through 562 Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.559A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 608 Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 668 through 685 Processing helix chain 'A' and resid 687 through 707 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 148 removed outlier: 4.064A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.584A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.914A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 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 307 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.523A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 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 removed outlier: 4.364A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.802A 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 481 through 507 Processing helix chain 'D' and resid 520 through 542 Processing helix chain 'D' and resid 546 through 562 removed outlier: 3.513A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.559A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 608 Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 668 through 685 Processing helix chain 'D' and resid 687 through 707 Processing helix chain 'D' and resid 708 through 716 Processing sheet with id=AA1, first strand: chain 'B' and resid 385 through 391 removed outlier: 3.619A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 385 through 391 removed outlier: 3.522A pdb=" N SER C 388 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 391 removed outlier: 3.619A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 385 through 391 removed outlier: 3.619A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3387 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: 2.74 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.41: 7843 1.41 - 1.73: 11140 1.73 - 2.04: 188 2.04 - 2.36: 0 2.36 - 2.68: 1 Bond restraints: 19172 Sorted by residual: bond pdb=" C PRO D 613 " pdb=" N LYS D 617 " ideal model delta sigma weight residual 1.332 2.681 -1.349 1.40e-02 5.10e+03 9.29e+03 bond pdb=" C20 EQK A1506 " pdb=" S01 EQK A1506 " ideal model delta sigma weight residual 1.732 1.435 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C25 EQK A1506 " pdb=" S01 EQK A1506 " ideal model delta sigma weight residual 1.727 1.467 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C20 EQK B1406 " pdb=" S01 EQK B1406 " ideal model delta sigma weight residual 1.732 1.496 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C20 EQK C1101 " pdb=" S01 EQK C1101 " ideal model delta sigma weight residual 1.732 1.496 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 19167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.39: 25976 10.39 - 20.78: 11 20.78 - 31.18: 1 31.18 - 41.57: 0 41.57 - 51.96: 1 Bond angle restraints: 25989 Sorted by residual: angle pdb=" O PRO D 613 " pdb=" C PRO D 613 " pdb=" N LYS D 617 " ideal model delta sigma weight residual 122.64 70.68 51.96 1.35e+00 5.49e-01 1.48e+03 angle pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N LYS D 617 " ideal model delta sigma weight residual 116.70 142.82 -26.12 2.07e+00 2.33e-01 1.59e+02 angle pdb=" CA ASP C 627 " pdb=" CB ASP C 627 " pdb=" CG ASP C 627 " ideal model delta sigma weight residual 112.60 119.94 -7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C LEU C 630 " pdb=" N GLU C 631 " pdb=" CA GLU C 631 " ideal model delta sigma weight residual 120.28 129.55 -9.27 1.34e+00 5.57e-01 4.78e+01 angle pdb=" C20 EQK A1506 " pdb=" S01 EQK A1506 " pdb=" C25 EQK A1506 " ideal model delta sigma weight residual 88.77 109.41 -20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 25984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 10825 35.16 - 70.31: 429 70.31 - 105.47: 33 105.47 - 140.63: 6 140.63 - 175.78: 1 Dihedral angle restraints: 11294 sinusoidal: 4165 harmonic: 7129 Sorted by residual: dihedral pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N LYS D 617 " pdb=" CA LYS D 617 " ideal model delta harmonic sigma weight residual -180.00 -64.48 -115.52 0 5.00e+00 4.00e-02 5.34e+02 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -156.67 70.67 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" N TRP B 380 " pdb=" C TRP B 380 " pdb=" CA TRP B 380 " pdb=" CB TRP B 380 " ideal model delta harmonic sigma weight residual 122.80 137.72 -14.92 0 2.50e+00 1.60e-01 3.56e+01 ... (remaining 11291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 2871 0.136 - 0.272: 166 0.272 - 0.408: 17 0.408 - 0.543: 3 0.543 - 0.679: 4 Chirality restraints: 3061 Sorted by residual: chirality pdb=" CA TRP B 380 " pdb=" N TRP B 380 " pdb=" C TRP B 380 " pdb=" CB TRP B 380 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA TRP C 380 " pdb=" N TRP C 380 " pdb=" C TRP C 380 " pdb=" CB TRP C 380 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA TRP D 380 " pdb=" N TRP D 380 " pdb=" C TRP D 380 " pdb=" CB TRP D 380 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 3058 not shown) Planarity restraints: 3169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 613 " -0.156 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C PRO D 613 " 0.313 2.00e-02 2.50e+03 pdb=" O PRO D 613 " -0.093 2.00e-02 2.50e+03 pdb=" N LYS D 617 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 EQK A1506 " -0.078 2.00e-02 2.50e+03 4.61e-02 4.25e+01 pdb=" C20 EQK A1506 " 0.076 2.00e-02 2.50e+03 pdb=" C22 EQK A1506 " 0.001 2.00e-02 2.50e+03 pdb=" C25 EQK A1506 " 0.026 2.00e-02 2.50e+03 pdb=" C26 EQK A1506 " 0.003 2.00e-02 2.50e+03 pdb=" N09 EQK A1506 " -0.020 2.00e-02 2.50e+03 pdb=" N10 EQK A1506 " -0.048 2.00e-02 2.50e+03 pdb=" S01 EQK A1506 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 EQK A1506 " -0.020 2.00e-02 2.50e+03 3.75e-02 2.82e+01 pdb=" C15 EQK A1506 " 0.004 2.00e-02 2.50e+03 pdb=" C16 EQK A1506 " 0.080 2.00e-02 2.50e+03 pdb=" C17 EQK A1506 " 0.020 2.00e-02 2.50e+03 pdb=" C20 EQK A1506 " -0.062 2.00e-02 2.50e+03 pdb=" C21 EQK A1506 " -0.006 2.00e-02 2.50e+03 pdb=" C24 EQK A1506 " -0.001 2.00e-02 2.50e+03 pdb=" N08 EQK A1506 " -0.016 2.00e-02 2.50e+03 ... (remaining 3166 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2971 2.74 - 3.28: 18536 3.28 - 3.82: 32299 3.82 - 4.36: 41210 4.36 - 4.90: 68097 Nonbonded interactions: 163113 Sorted by model distance: nonbonded pdb=" OH TYR C 382 " pdb=" OD1 ASN D 220 " model vdw 2.206 3.040 nonbonded pdb=" O VAL D 596 " pdb=" C31 EQK D1101 " model vdw 2.214 3.340 nonbonded pdb=" OG SER C 620 " pdb=" O GLN C 646 " model vdw 2.235 3.040 nonbonded pdb=" O VAL B 596 " pdb=" C31 EQK B1406 " model vdw 2.238 3.340 nonbonded pdb=" ND2 ASN D 298 " pdb=" OG1 THR D 336 " model vdw 2.240 3.120 ... (remaining 163108 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 713 or (resid 714 and (name N or name CA or na \ me C or name O or name CB )) or resid 715 through 754 or (resid 1503 and (name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44 or name C45 or name C46 or name C47 or name C48 or name C49)) or (resid 1 \ 504 and (name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or \ name C43 or name C44 or name C45 or name C46 or name C47)) or (resid 1505 and ( \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C46 or name C47 or name C48 or name \ C49)))) selection = (chain 'B' and (resid 118 through 334 or (resid 335 and (name N or name CA or na \ me C or name O or name CB )) or resid 336 through 614 or resid 618 through 749 o \ r (resid 750 through 752 and (name N or name CA or name C or name O or name CB ) \ ) or resid 753 through 754 or (resid 1403 and (name C37 or name C38 or name C39 \ or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name \ C46 or name C47 or name C48 or name C49)) or (resid 1404 and (name C37 or name C \ 38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or na \ me C45 or name C46 or name C47)) or (resid 1405 and (name C36 or name C37 or nam \ e C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C46 or name C47 or name C48 or name C49)))) selection = (chain 'C' and (resid 118 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB )) or resid 419 through 614 or resid 618 through 754 o \ r resid 1103 or (resid 1104 and (name C37 or name C38 or name C39 or name C40 or \ name C41 or name C42 or name C43 or name C44 or name C45 or name C46 or name C4 \ 7)) or resid 1105)) selection = (chain 'D' and (resid 118 through 749 or (resid 750 through 752 and (name N or n \ ame CA or name C or name O or name CB )) or resid 753 through 754 or (resid 1103 \ and (name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or na \ me C43 or name C44 or name C45 or name C46 or name C47 or name C48 or name C49)) \ or (resid 1104 and (name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42 or name C43 or name C44 or name C45 or name C46 or name C47)) or (resi \ d 1105 and (name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name C42 or name C43 or name C44 or name C45 or name C46 or name C47 or name \ C48 or name C49)))) } 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: 2.650 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.630 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.021 1.349 19173 Z= 1.119 Angle : 1.395 51.961 25991 Z= 0.780 Chirality : 0.078 0.679 3061 Planarity : 0.007 0.184 3169 Dihedral : 18.349 175.784 6659 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.95 % Favored : 93.01 % Rotamer: Outliers : 6.56 % Allowed : 13.86 % Favored : 79.59 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.14), residues: 2388 helix: -1.91 (0.10), residues: 1602 sheet: -3.05 (0.44), residues: 68 loop : -2.87 (0.19), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 729 TYR 0.053 0.005 TYR A 260 PHE 0.027 0.004 PHE D 633 TRP 0.021 0.004 TRP B 380 HIS 0.014 0.003 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.01969 (19172) covalent geometry : angle 1.35905 (25989) SS BOND : bond 0.81386 ( 1) SS BOND : angle 35.69549 ( 2) hydrogen bonds : bond 0.15644 ( 1137) hydrogen bonds : angle 7.54970 ( 3387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 288 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.5445 (mmt) cc_final: 0.5139 (mmp) REVERT: B 173 MET cc_start: 0.6645 (mtt) cc_final: 0.5797 (mtm) REVERT: B 179 ILE cc_start: 0.5661 (OUTLIER) cc_final: 0.5460 (pp) REVERT: B 327 ARG cc_start: 0.7016 (tpp80) cc_final: 0.6790 (tpp-160) REVERT: B 340 ASP cc_start: 0.7528 (t70) cc_final: 0.7084 (t0) REVERT: B 371 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6448 (ttt180) REVERT: B 426 HIS cc_start: 0.7818 (t70) cc_final: 0.7577 (t-90) REVERT: B 434 LYS cc_start: 0.7918 (mttt) cc_final: 0.7714 (mttp) REVERT: B 495 MET cc_start: 0.7287 (mtm) cc_final: 0.7080 (mtt) REVERT: B 545 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7024 (mmtt) REVERT: B 555 MET cc_start: 0.8114 (tmm) cc_final: 0.7727 (tmm) REVERT: B 677 MET cc_start: 0.8796 (mtt) cc_final: 0.8521 (mtt) REVERT: B 682 GLU cc_start: 0.7629 (pt0) cc_final: 0.7304 (pp20) REVERT: B 706 MET cc_start: 0.8290 (mtt) cc_final: 0.7908 (mtt) REVERT: C 157 PHE cc_start: 0.4565 (OUTLIER) cc_final: 0.3774 (m-10) REVERT: C 173 MET cc_start: 0.6458 (mtt) cc_final: 0.5712 (mtm) REVERT: C 214 GLU cc_start: 0.5591 (tt0) cc_final: 0.4797 (mp0) REVERT: C 340 ASP cc_start: 0.7361 (t70) cc_final: 0.6894 (t0) REVERT: C 419 MET cc_start: 0.8532 (mtm) cc_final: 0.8103 (mtm) REVERT: C 492 ILE cc_start: 0.7692 (pt) cc_final: 0.7402 (mt) REVERT: C 540 TYR cc_start: 0.7760 (t80) cc_final: 0.7533 (t80) REVERT: C 555 MET cc_start: 0.8008 (tmm) cc_final: 0.7681 (tmm) REVERT: C 574 MET cc_start: 0.8382 (mtp) cc_final: 0.8173 (mtp) REVERT: C 610 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7139 (mt-10) REVERT: C 677 MET cc_start: 0.8699 (mtt) cc_final: 0.8438 (mtt) REVERT: C 682 GLU cc_start: 0.7508 (pt0) cc_final: 0.7205 (pp20) REVERT: C 706 MET cc_start: 0.8372 (mtt) cc_final: 0.7852 (mtt) REVERT: A 157 PHE cc_start: 0.4528 (OUTLIER) cc_final: 0.3976 (m-10) REVERT: A 173 MET cc_start: 0.6850 (mtt) cc_final: 0.6294 (mtm) REVERT: A 179 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.5348 (pp) REVERT: A 214 GLU cc_start: 0.5790 (tt0) cc_final: 0.5465 (tt0) REVERT: A 337 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6801 (mtp85) REVERT: A 340 ASP cc_start: 0.7422 (t70) cc_final: 0.6926 (t0) REVERT: A 366 LYS cc_start: 0.5642 (OUTLIER) cc_final: 0.4562 (ptpp) REVERT: A 419 MET cc_start: 0.8309 (mtm) cc_final: 0.7960 (mtm) REVERT: A 434 LYS cc_start: 0.7948 (mttt) cc_final: 0.7736 (mttp) REVERT: A 540 TYR cc_start: 0.7747 (t80) cc_final: 0.7524 (t80) REVERT: A 555 MET cc_start: 0.8009 (tmm) cc_final: 0.7667 (tmm) REVERT: A 677 MET cc_start: 0.8763 (mtt) cc_final: 0.8412 (mtt) REVERT: A 682 GLU cc_start: 0.7714 (pt0) cc_final: 0.7448 (pp20) REVERT: A 689 GLU cc_start: 0.8055 (tt0) cc_final: 0.7784 (tt0) REVERT: D 157 PHE cc_start: 0.4308 (OUTLIER) cc_final: 0.4103 (m-10) REVERT: D 159 MET cc_start: 0.5476 (mmt) cc_final: 0.5212 (mmp) REVERT: D 214 GLU cc_start: 0.5638 (tt0) cc_final: 0.4707 (mp0) REVERT: D 340 ASP cc_start: 0.7563 (t70) cc_final: 0.7114 (t0) REVERT: D 366 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.4777 (ttpp) REVERT: D 540 TYR cc_start: 0.7471 (t80) cc_final: 0.7234 (t80) REVERT: D 677 MET cc_start: 0.8685 (mtt) cc_final: 0.8428 (mtt) REVERT: D 682 GLU cc_start: 0.7769 (pt0) cc_final: 0.7430 (pp20) REVERT: D 689 GLU cc_start: 0.7993 (tt0) cc_final: 0.7709 (tt0) REVERT: D 706 MET cc_start: 0.8400 (mtt) cc_final: 0.8072 (mtt) outliers start: 114 outliers final: 49 residues processed: 380 average time/residue: 0.5568 time to fit residues: 239.3023 Evaluate side-chains 302 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 380 TRP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 380 TRP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 635 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 284 HIS B 301 HIS B 339 ASN B 346 GLN B 394 ASN B 452 ASN B 580 GLN B 646 GLN B 647 ASN C 178 ASN C 197 ASN C 284 HIS C 301 HIS C 339 ASN C 346 GLN C 394 ASN C 430 HIS C 452 ASN C 580 GLN C 646 GLN C 647 ASN A 178 ASN A 197 ASN A 301 HIS A 339 ASN A 452 ASN A 580 GLN A 646 GLN D 178 ASN D 197 ASN D 301 HIS D 339 ASN D 346 GLN D 452 ASN D 580 GLN D 646 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.212744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144951 restraints weight = 17160.412| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.75 r_work: 0.3496 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19173 Z= 0.157 Angle : 0.602 7.466 25991 Z= 0.314 Chirality : 0.039 0.180 3061 Planarity : 0.004 0.057 3169 Dihedral : 14.197 164.160 3037 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.39 % Allowed : 16.10 % Favored : 80.51 % 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 (0.16), residues: 2390 helix: -0.05 (0.12), residues: 1642 sheet: -2.86 (0.50), residues: 68 loop : -2.43 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 693 TYR 0.023 0.002 TYR C 451 PHE 0.015 0.002 PHE D 377 TRP 0.028 0.002 TRP A 380 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00353 (19172) covalent geometry : angle 0.60171 (25989) SS BOND : bond 0.00792 ( 1) SS BOND : angle 2.25470 ( 2) hydrogen bonds : bond 0.04203 ( 1137) hydrogen bonds : angle 4.94036 ( 3387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 MET cc_start: 0.8320 (tpp) cc_final: 0.8078 (tpp) REVERT: B 327 ARG cc_start: 0.6903 (tpp80) cc_final: 0.6617 (tpp-160) REVERT: B 340 ASP cc_start: 0.7755 (t70) cc_final: 0.7207 (t0) REVERT: B 371 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6238 (tpt170) REVERT: B 426 HIS cc_start: 0.8124 (t70) cc_final: 0.7857 (t-90) REVERT: B 434 LYS cc_start: 0.8302 (mttt) cc_final: 0.7627 (mttp) REVERT: B 488 MET cc_start: 0.7450 (mtm) cc_final: 0.6822 (mmm) REVERT: B 499 VAL cc_start: 0.7524 (m) cc_final: 0.7214 (t) REVERT: B 645 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7731 (mt0) REVERT: B 682 GLU cc_start: 0.8049 (pt0) cc_final: 0.7569 (pp20) REVERT: B 689 GLU cc_start: 0.8304 (tt0) cc_final: 0.8102 (tt0) REVERT: B 693 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7437 (ttm-80) REVERT: B 704 GLU cc_start: 0.8228 (tt0) cc_final: 0.8017 (tt0) REVERT: B 706 MET cc_start: 0.8158 (mtt) cc_final: 0.7844 (mtp) REVERT: C 159 MET cc_start: 0.4758 (mmt) cc_final: 0.4455 (mmp) REVERT: C 173 MET cc_start: 0.5804 (mtt) cc_final: 0.5562 (mtt) REVERT: C 327 ARG cc_start: 0.6633 (tpp80) cc_final: 0.6034 (tmt170) REVERT: C 340 ASP cc_start: 0.7621 (t70) cc_final: 0.7101 (t0) REVERT: C 419 MET cc_start: 0.8371 (mtm) cc_final: 0.7954 (mtm) REVERT: C 434 LYS cc_start: 0.8292 (mttt) cc_final: 0.7394 (ttpp) REVERT: C 540 TYR cc_start: 0.7880 (t80) cc_final: 0.7669 (t80) REVERT: C 546 GLU cc_start: 0.8203 (mp0) cc_final: 0.7992 (mp0) REVERT: C 610 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 682 GLU cc_start: 0.8069 (pt0) cc_final: 0.7646 (pp20) REVERT: C 689 GLU cc_start: 0.8217 (tt0) cc_final: 0.7972 (tt0) REVERT: C 693 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7384 (ttm-80) REVERT: C 706 MET cc_start: 0.8135 (mtt) cc_final: 0.7825 (mtp) REVERT: A 173 MET cc_start: 0.6124 (mtt) cc_final: 0.5730 (mtm) REVERT: A 340 ASP cc_start: 0.7582 (t70) cc_final: 0.7022 (t0) REVERT: A 371 ARG cc_start: 0.5917 (tpt170) cc_final: 0.5707 (tpt170) REVERT: A 419 MET cc_start: 0.8104 (mtm) cc_final: 0.7573 (mtm) REVERT: A 434 LYS cc_start: 0.8256 (mttt) cc_final: 0.7582 (mttp) REVERT: A 495 MET cc_start: 0.7869 (mtm) cc_final: 0.7507 (mtp) REVERT: A 645 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7607 (mt0) REVERT: A 677 MET cc_start: 0.8915 (mtt) cc_final: 0.8706 (mtt) REVERT: A 682 GLU cc_start: 0.8231 (pt0) cc_final: 0.7783 (pp20) REVERT: A 693 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.6936 (mtm110) REVERT: A 704 GLU cc_start: 0.8148 (tt0) cc_final: 0.7894 (tt0) REVERT: D 173 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6235 (mtm) REVERT: D 340 ASP cc_start: 0.7765 (t70) cc_final: 0.7335 (t0) REVERT: D 366 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.4835 (ttpp) REVERT: D 434 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7518 (mppt) REVERT: D 488 MET cc_start: 0.7277 (mtm) cc_final: 0.6736 (mmm) REVERT: D 540 TYR cc_start: 0.7695 (t80) cc_final: 0.7429 (t80) REVERT: D 610 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7651 (mt-10) REVERT: D 631 GLU cc_start: 0.7614 (pt0) cc_final: 0.7051 (mt-10) REVERT: D 682 GLU cc_start: 0.8148 (pt0) cc_final: 0.7648 (pp20) REVERT: D 706 MET cc_start: 0.8321 (mtt) cc_final: 0.7914 (mtp) outliers start: 59 outliers final: 19 residues processed: 344 average time/residue: 0.5308 time to fit residues: 207.4118 Evaluate side-chains 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.0970 chunk 232 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS A 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144145 restraints weight = 17436.917| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.60 r_work: 0.3508 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19173 Z= 0.125 Angle : 0.534 5.995 25991 Z= 0.282 Chirality : 0.037 0.154 3061 Planarity : 0.004 0.057 3169 Dihedral : 12.787 164.212 2972 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.88 % Allowed : 17.02 % Favored : 80.10 % 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: -0.34 (0.17), residues: 2390 helix: 0.63 (0.13), residues: 1654 sheet: -2.56 (0.49), residues: 68 loop : -2.05 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 693 TYR 0.022 0.002 TYR A 451 PHE 0.012 0.001 PHE A 666 TRP 0.030 0.002 TRP B 380 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00274 (19172) covalent geometry : angle 0.53363 (25989) SS BOND : bond 0.00301 ( 1) SS BOND : angle 1.34695 ( 2) hydrogen bonds : bond 0.03791 ( 1137) hydrogen bonds : angle 4.48236 ( 3387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 MET cc_start: 0.8231 (tpp) cc_final: 0.8010 (tpp) REVERT: B 340 ASP cc_start: 0.7688 (t70) cc_final: 0.7198 (t0) REVERT: B 371 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6102 (tpt170) REVERT: B 419 MET cc_start: 0.8225 (mtm) cc_final: 0.7729 (mtm) REVERT: B 434 LYS cc_start: 0.8212 (mttt) cc_final: 0.7263 (ttpp) REVERT: B 488 MET cc_start: 0.7470 (mtm) cc_final: 0.6855 (mmm) REVERT: B 645 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7692 (mt0) REVERT: B 652 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8380 (mm) REVERT: B 682 GLU cc_start: 0.7995 (pt0) cc_final: 0.7550 (pp20) REVERT: B 693 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7289 (ttp-110) REVERT: B 706 MET cc_start: 0.8057 (mtt) cc_final: 0.7721 (mtp) REVERT: C 159 MET cc_start: 0.5034 (mmt) cc_final: 0.4727 (mmp) REVERT: C 337 ARG cc_start: 0.7234 (mtp85) cc_final: 0.6868 (mtp85) REVERT: C 340 ASP cc_start: 0.7565 (t70) cc_final: 0.7030 (t0) REVERT: C 419 MET cc_start: 0.8381 (mtm) cc_final: 0.8002 (mtm) REVERT: C 434 LYS cc_start: 0.8232 (mttt) cc_final: 0.7279 (ttpp) REVERT: C 495 MET cc_start: 0.7707 (mtm) cc_final: 0.7326 (mtp) REVERT: C 546 GLU cc_start: 0.8101 (mp0) cc_final: 0.7893 (mp0) REVERT: C 682 GLU cc_start: 0.7913 (pt0) cc_final: 0.7452 (pp20) REVERT: C 689 GLU cc_start: 0.8181 (tt0) cc_final: 0.7957 (tt0) REVERT: A 173 MET cc_start: 0.6073 (mtt) cc_final: 0.5728 (mtm) REVERT: A 340 ASP cc_start: 0.7609 (t70) cc_final: 0.7094 (t0) REVERT: A 419 MET cc_start: 0.8125 (mtm) cc_final: 0.7595 (mtm) REVERT: A 434 LYS cc_start: 0.8206 (mttt) cc_final: 0.7238 (ttpp) REVERT: A 443 LEU cc_start: 0.8534 (tp) cc_final: 0.8325 (tp) REVERT: A 495 MET cc_start: 0.7794 (mtm) cc_final: 0.7426 (mtp) REVERT: A 555 MET cc_start: 0.7773 (tmm) cc_final: 0.7559 (tmm) REVERT: A 584 LEU cc_start: 0.8365 (mt) cc_final: 0.8140 (mm) REVERT: A 645 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7620 (mt0) REVERT: A 677 MET cc_start: 0.8928 (mtt) cc_final: 0.8715 (mtt) REVERT: A 682 GLU cc_start: 0.8133 (pt0) cc_final: 0.7714 (pp20) REVERT: A 693 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.6876 (mtm110) REVERT: A 732 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7154 (tp) REVERT: D 173 MET cc_start: 0.6632 (mtm) cc_final: 0.6427 (mtm) REVERT: D 340 ASP cc_start: 0.7701 (t70) cc_final: 0.7210 (t0) REVERT: D 426 HIS cc_start: 0.8116 (t70) cc_final: 0.7874 (t-90) REVERT: D 434 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7422 (mppt) REVERT: D 488 MET cc_start: 0.7264 (mtm) cc_final: 0.6696 (mmm) REVERT: D 540 TYR cc_start: 0.7622 (t80) cc_final: 0.7395 (t80) REVERT: D 631 GLU cc_start: 0.7530 (pt0) cc_final: 0.6969 (mm-30) REVERT: D 682 GLU cc_start: 0.8040 (pt0) cc_final: 0.7640 (pp20) REVERT: D 706 MET cc_start: 0.8160 (mtt) cc_final: 0.7777 (mtp) outliers start: 50 outliers final: 13 residues processed: 315 average time/residue: 0.5666 time to fit residues: 201.2887 Evaluate side-chains 285 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.0070 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 HIS C 430 HIS A 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.215750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149561 restraints weight = 17430.859| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.27 r_work: 0.3504 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19173 Z= 0.112 Angle : 0.501 5.743 25991 Z= 0.264 Chirality : 0.036 0.142 3061 Planarity : 0.004 0.057 3169 Dihedral : 11.919 164.368 2959 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.99 % Allowed : 18.52 % Favored : 78.49 % 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: 0.21 (0.17), residues: 2390 helix: 1.01 (0.13), residues: 1652 sheet: -1.79 (0.52), residues: 68 loop : -1.80 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.022 0.002 TYR B 451 PHE 0.012 0.001 PHE A 666 TRP 0.027 0.001 TRP B 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00243 (19172) covalent geometry : angle 0.50096 (25989) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.75301 ( 2) hydrogen bonds : bond 0.03546 ( 1137) hydrogen bonds : angle 4.22524 ( 3387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7043 (t0) cc_final: 0.6338 (p0) REVERT: B 320 MET cc_start: 0.8329 (tpp) cc_final: 0.8108 (tpp) REVERT: B 340 ASP cc_start: 0.7724 (t70) cc_final: 0.7199 (t0) REVERT: B 371 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6158 (tpt170) REVERT: B 419 MET cc_start: 0.8288 (mtm) cc_final: 0.7751 (mtm) REVERT: B 426 HIS cc_start: 0.8269 (t70) cc_final: 0.7968 (t-90) REVERT: B 434 LYS cc_start: 0.8308 (mttt) cc_final: 0.7368 (ttpp) REVERT: B 488 MET cc_start: 0.7351 (mtm) cc_final: 0.6762 (mmm) REVERT: B 645 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7732 (mt0) REVERT: B 652 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 682 GLU cc_start: 0.8073 (pt0) cc_final: 0.7639 (pp20) REVERT: C 159 MET cc_start: 0.5004 (mmt) cc_final: 0.4715 (mmp) REVERT: C 340 ASP cc_start: 0.7613 (t70) cc_final: 0.7078 (t0) REVERT: C 371 ARG cc_start: 0.6571 (tpt170) cc_final: 0.6343 (tpt170) REVERT: C 419 MET cc_start: 0.8373 (mtm) cc_final: 0.8012 (mtm) REVERT: C 434 LYS cc_start: 0.8295 (mttt) cc_final: 0.7388 (ttpp) REVERT: C 488 MET cc_start: 0.7485 (mtm) cc_final: 0.6805 (mmm) REVERT: C 495 MET cc_start: 0.7813 (mtm) cc_final: 0.7395 (mtp) REVERT: C 546 GLU cc_start: 0.8143 (mp0) cc_final: 0.7907 (mp0) REVERT: C 682 GLU cc_start: 0.7922 (pt0) cc_final: 0.7454 (pp20) REVERT: A 340 ASP cc_start: 0.7681 (t70) cc_final: 0.7118 (t0) REVERT: A 419 MET cc_start: 0.8131 (mtm) cc_final: 0.7597 (mtm) REVERT: A 434 LYS cc_start: 0.8309 (mttt) cc_final: 0.7338 (ttpp) REVERT: A 495 MET cc_start: 0.7865 (mtm) cc_final: 0.7487 (mtp) REVERT: A 645 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7640 (mt0) REVERT: A 682 GLU cc_start: 0.8167 (pt0) cc_final: 0.7744 (pp20) REVERT: A 706 MET cc_start: 0.7916 (mtp) cc_final: 0.7638 (mtp) REVERT: A 732 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7065 (tp) REVERT: D 330 ASN cc_start: 0.7310 (p0) cc_final: 0.7108 (p0) REVERT: D 340 ASP cc_start: 0.7595 (t70) cc_final: 0.7119 (t0) REVERT: D 426 HIS cc_start: 0.8245 (t70) cc_final: 0.7979 (t-90) REVERT: D 434 LYS cc_start: 0.8340 (mmtp) cc_final: 0.7482 (mppt) REVERT: D 488 MET cc_start: 0.7175 (mtm) cc_final: 0.6661 (mmm) REVERT: D 540 TYR cc_start: 0.7682 (t80) cc_final: 0.7448 (t80) REVERT: D 546 GLU cc_start: 0.8122 (mp0) cc_final: 0.7881 (mp0) REVERT: D 584 LEU cc_start: 0.8451 (mt) cc_final: 0.8181 (mm) REVERT: D 631 GLU cc_start: 0.7580 (pt0) cc_final: 0.7028 (mm-30) REVERT: D 682 GLU cc_start: 0.8117 (pt0) cc_final: 0.7707 (pp20) outliers start: 52 outliers final: 7 residues processed: 319 average time/residue: 0.5543 time to fit residues: 199.5537 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 266 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 HIS C 430 HIS A 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.215572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148434 restraints weight = 17406.037| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.06 r_work: 0.3506 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19173 Z= 0.125 Angle : 0.512 7.695 25991 Z= 0.269 Chirality : 0.037 0.151 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.822 163.981 2954 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.30 % Allowed : 20.47 % Favored : 77.23 % 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: 0.37 (0.17), residues: 2390 helix: 1.16 (0.13), residues: 1640 sheet: -1.48 (0.54), residues: 72 loop : -1.80 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 693 TYR 0.021 0.002 TYR D 451 PHE 0.013 0.001 PHE A 445 TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00284 (19172) covalent geometry : angle 0.51243 (25989) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.78180 ( 2) hydrogen bonds : bond 0.03615 ( 1137) hydrogen bonds : angle 4.20102 ( 3387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7014 (t0) cc_final: 0.6333 (p0) REVERT: B 320 MET cc_start: 0.8310 (tpp) cc_final: 0.8067 (tpp) REVERT: B 327 ARG cc_start: 0.6692 (tpp-160) cc_final: 0.6241 (ttm170) REVERT: B 340 ASP cc_start: 0.7664 (t70) cc_final: 0.7120 (t0) REVERT: B 371 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6196 (tpt170) REVERT: B 419 MET cc_start: 0.8276 (mtm) cc_final: 0.7747 (mtm) REVERT: B 426 HIS cc_start: 0.8210 (t70) cc_final: 0.7937 (t-90) REVERT: B 434 LYS cc_start: 0.8263 (mttt) cc_final: 0.7350 (ttpp) REVERT: B 488 MET cc_start: 0.7382 (mtm) cc_final: 0.6816 (mmm) REVERT: B 584 LEU cc_start: 0.8441 (mt) cc_final: 0.8205 (mm) REVERT: B 645 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7711 (mt0) REVERT: B 652 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 682 GLU cc_start: 0.8060 (pt0) cc_final: 0.7633 (pp20) REVERT: C 159 MET cc_start: 0.5069 (mmt) cc_final: 0.4773 (mmp) REVERT: C 340 ASP cc_start: 0.7602 (t70) cc_final: 0.7068 (t0) REVERT: C 371 ARG cc_start: 0.6482 (tpt170) cc_final: 0.6281 (tpt170) REVERT: C 419 MET cc_start: 0.8376 (mtm) cc_final: 0.7992 (mtm) REVERT: C 434 LYS cc_start: 0.8309 (mttt) cc_final: 0.7394 (ttpp) REVERT: C 488 MET cc_start: 0.7529 (mtm) cc_final: 0.6871 (mmm) REVERT: C 495 MET cc_start: 0.7831 (mtm) cc_final: 0.7425 (mtp) REVERT: C 546 GLU cc_start: 0.8110 (mp0) cc_final: 0.7862 (mp0) REVERT: C 682 GLU cc_start: 0.7918 (pt0) cc_final: 0.7510 (pp20) REVERT: C 693 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: A 179 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.4821 (pp) REVERT: A 340 ASP cc_start: 0.7681 (t70) cc_final: 0.7111 (t0) REVERT: A 419 MET cc_start: 0.8111 (mtm) cc_final: 0.7607 (mtm) REVERT: A 434 LYS cc_start: 0.8291 (mttt) cc_final: 0.7335 (ttpp) REVERT: A 495 MET cc_start: 0.7799 (mtm) cc_final: 0.7433 (mtp) REVERT: A 645 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7648 (mt0) REVERT: A 682 GLU cc_start: 0.8132 (pt0) cc_final: 0.7700 (pp20) REVERT: A 693 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.6975 (mtm110) REVERT: A 732 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7049 (tp) REVERT: D 330 ASN cc_start: 0.7296 (p0) cc_final: 0.7078 (p0) REVERT: D 340 ASP cc_start: 0.7696 (t70) cc_final: 0.7204 (t0) REVERT: D 426 HIS cc_start: 0.8192 (t70) cc_final: 0.7942 (t-90) REVERT: D 434 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7534 (mppt) REVERT: D 488 MET cc_start: 0.7217 (mtm) cc_final: 0.6716 (mmm) REVERT: D 540 TYR cc_start: 0.7696 (t80) cc_final: 0.7484 (t80) REVERT: D 546 GLU cc_start: 0.8109 (mp0) cc_final: 0.7867 (mp0) REVERT: D 584 LEU cc_start: 0.8427 (mt) cc_final: 0.8195 (mm) REVERT: D 631 GLU cc_start: 0.7588 (pt0) cc_final: 0.7167 (mm-30) REVERT: D 682 GLU cc_start: 0.8106 (pt0) cc_final: 0.7699 (pp20) REVERT: D 693 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7307 (ttm-80) outliers start: 40 outliers final: 14 residues processed: 300 average time/residue: 0.5356 time to fit residues: 181.2015 Evaluate side-chains 285 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN B 346 GLN B 430 HIS B 523 HIS C 430 HIS C 645 GLN A 430 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.215498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144743 restraints weight = 17252.150| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.69 r_work: 0.3524 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19173 Z= 0.126 Angle : 0.512 7.693 25991 Z= 0.268 Chirality : 0.037 0.151 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.826 163.980 2954 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.09 % Allowed : 21.97 % Favored : 76.94 % 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: 0.37 (0.17), residues: 2390 helix: 1.16 (0.13), residues: 1640 sheet: -1.48 (0.54), residues: 72 loop : -1.80 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 693 TYR 0.021 0.002 TYR D 451 PHE 0.013 0.001 PHE A 445 TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00284 (19172) covalent geometry : angle 0.51240 (25989) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.78183 ( 2) hydrogen bonds : bond 0.03615 ( 1137) hydrogen bonds : angle 4.20100 ( 3387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7009 (t0) cc_final: 0.6337 (p0) REVERT: B 320 MET cc_start: 0.8318 (tpp) cc_final: 0.8073 (tpp) REVERT: B 327 ARG cc_start: 0.6749 (tpp-160) cc_final: 0.6258 (ttm170) REVERT: B 340 ASP cc_start: 0.7654 (t70) cc_final: 0.7122 (t0) REVERT: B 371 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6197 (tpt170) REVERT: B 419 MET cc_start: 0.8272 (mtm) cc_final: 0.7738 (mtm) REVERT: B 426 HIS cc_start: 0.8210 (t70) cc_final: 0.7923 (t-90) REVERT: B 434 LYS cc_start: 0.8245 (mttt) cc_final: 0.7330 (ttpp) REVERT: B 488 MET cc_start: 0.7386 (mtm) cc_final: 0.6824 (mmm) REVERT: B 584 LEU cc_start: 0.8440 (mt) cc_final: 0.8209 (mm) REVERT: B 645 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7728 (mt0) REVERT: B 652 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8418 (mm) REVERT: B 682 GLU cc_start: 0.8030 (pt0) cc_final: 0.7611 (pp20) REVERT: C 159 MET cc_start: 0.5083 (mmt) cc_final: 0.4785 (mmp) REVERT: C 340 ASP cc_start: 0.7603 (t70) cc_final: 0.7072 (t0) REVERT: C 371 ARG cc_start: 0.6478 (tpt170) cc_final: 0.6278 (tpt170) REVERT: C 419 MET cc_start: 0.8366 (mtm) cc_final: 0.7991 (mtm) REVERT: C 434 LYS cc_start: 0.8281 (mttt) cc_final: 0.7370 (ttpp) REVERT: C 488 MET cc_start: 0.7516 (mtm) cc_final: 0.6872 (mmm) REVERT: C 495 MET cc_start: 0.7828 (mtm) cc_final: 0.7421 (mtp) REVERT: C 546 GLU cc_start: 0.8116 (mp0) cc_final: 0.7849 (mp0) REVERT: C 682 GLU cc_start: 0.7903 (pt0) cc_final: 0.7495 (pp20) REVERT: C 693 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: A 179 ILE cc_start: 0.5089 (OUTLIER) cc_final: 0.4825 (pp) REVERT: A 340 ASP cc_start: 0.7668 (t70) cc_final: 0.7105 (t0) REVERT: A 419 MET cc_start: 0.8097 (mtm) cc_final: 0.7611 (mtm) REVERT: A 434 LYS cc_start: 0.8277 (mttt) cc_final: 0.7329 (ttpp) REVERT: A 495 MET cc_start: 0.7797 (mtm) cc_final: 0.7435 (mtp) REVERT: A 645 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7674 (mt0) REVERT: A 682 GLU cc_start: 0.8117 (pt0) cc_final: 0.7692 (pp20) REVERT: A 693 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.6959 (mtm110) REVERT: A 732 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7036 (tp) REVERT: D 330 ASN cc_start: 0.7304 (p0) cc_final: 0.7084 (p0) REVERT: D 340 ASP cc_start: 0.7688 (t70) cc_final: 0.7202 (t0) REVERT: D 426 HIS cc_start: 0.8160 (t70) cc_final: 0.7915 (t-90) REVERT: D 434 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7510 (mppt) REVERT: D 488 MET cc_start: 0.7226 (mtm) cc_final: 0.6733 (mmm) REVERT: D 540 TYR cc_start: 0.7680 (t80) cc_final: 0.7472 (t80) REVERT: D 546 GLU cc_start: 0.8093 (mp0) cc_final: 0.7852 (mp0) REVERT: D 584 LEU cc_start: 0.8431 (mt) cc_final: 0.8203 (mm) REVERT: D 631 GLU cc_start: 0.7558 (pt0) cc_final: 0.7160 (mm-30) REVERT: D 682 GLU cc_start: 0.8067 (pt0) cc_final: 0.7665 (pp20) REVERT: D 693 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7292 (ttm-80) outliers start: 19 outliers final: 14 residues processed: 280 average time/residue: 0.5497 time to fit residues: 173.4849 Evaluate side-chains 284 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN B 430 HIS B 523 HIS C 430 HIS C 645 GLN A 430 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.215477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144696 restraints weight = 17281.706| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.69 r_work: 0.3525 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19173 Z= 0.126 Angle : 0.512 7.687 25991 Z= 0.268 Chirality : 0.037 0.150 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.835 163.980 2954 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.15 % Allowed : 21.97 % Favored : 76.88 % 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: 0.37 (0.17), residues: 2390 helix: 1.16 (0.13), residues: 1640 sheet: -1.48 (0.54), residues: 72 loop : -1.80 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 693 TYR 0.021 0.002 TYR D 451 PHE 0.013 0.001 PHE A 445 TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00285 (19172) covalent geometry : angle 0.51227 (25989) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.78171 ( 2) hydrogen bonds : bond 0.03616 ( 1137) hydrogen bonds : angle 4.20096 ( 3387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7004 (t0) cc_final: 0.6327 (p0) REVERT: B 320 MET cc_start: 0.8289 (tpp) cc_final: 0.8041 (tpp) REVERT: B 327 ARG cc_start: 0.6737 (tpp-160) cc_final: 0.6244 (ttm170) REVERT: B 340 ASP cc_start: 0.7647 (t70) cc_final: 0.7104 (t0) REVERT: B 371 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6182 (tpt170) REVERT: B 419 MET cc_start: 0.8271 (mtm) cc_final: 0.7735 (mtm) REVERT: B 426 HIS cc_start: 0.8210 (t70) cc_final: 0.7923 (t-90) REVERT: B 434 LYS cc_start: 0.8239 (mttt) cc_final: 0.7325 (ttpp) REVERT: B 488 MET cc_start: 0.7382 (mtm) cc_final: 0.6816 (mmm) REVERT: B 584 LEU cc_start: 0.8437 (mt) cc_final: 0.8205 (mm) REVERT: B 645 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7714 (mt0) REVERT: B 652 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 682 GLU cc_start: 0.8028 (pt0) cc_final: 0.7600 (pp20) REVERT: C 159 MET cc_start: 0.5017 (mmt) cc_final: 0.4725 (mmp) REVERT: C 340 ASP cc_start: 0.7592 (t70) cc_final: 0.7055 (t0) REVERT: C 371 ARG cc_start: 0.6464 (tpt170) cc_final: 0.6263 (tpt170) REVERT: C 419 MET cc_start: 0.8365 (mtm) cc_final: 0.7989 (mtm) REVERT: C 434 LYS cc_start: 0.8277 (mttt) cc_final: 0.7368 (ttpp) REVERT: C 488 MET cc_start: 0.7510 (mtm) cc_final: 0.6863 (mmm) REVERT: C 495 MET cc_start: 0.7818 (mtm) cc_final: 0.7411 (mtp) REVERT: C 546 GLU cc_start: 0.8113 (mp0) cc_final: 0.7849 (mp0) REVERT: C 682 GLU cc_start: 0.7895 (pt0) cc_final: 0.7480 (pp20) REVERT: C 693 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7334 (ttm-80) REVERT: A 179 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4786 (pp) REVERT: A 340 ASP cc_start: 0.7657 (t70) cc_final: 0.7086 (t0) REVERT: A 419 MET cc_start: 0.8096 (mtm) cc_final: 0.7611 (mtm) REVERT: A 434 LYS cc_start: 0.8273 (mttt) cc_final: 0.7321 (ttpp) REVERT: A 495 MET cc_start: 0.7784 (mtm) cc_final: 0.7422 (mtp) REVERT: A 645 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7660 (mt0) REVERT: A 682 GLU cc_start: 0.8118 (pt0) cc_final: 0.7686 (pp20) REVERT: A 693 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.6950 (mtm110) REVERT: A 732 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7017 (tp) REVERT: D 330 ASN cc_start: 0.7282 (p0) cc_final: 0.7064 (p0) REVERT: D 340 ASP cc_start: 0.7681 (t70) cc_final: 0.7186 (t0) REVERT: D 426 HIS cc_start: 0.8162 (t70) cc_final: 0.7916 (t-90) REVERT: D 434 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7510 (mppt) REVERT: D 488 MET cc_start: 0.7212 (mtm) cc_final: 0.6718 (mmm) REVERT: D 540 TYR cc_start: 0.7692 (t80) cc_final: 0.7484 (t80) REVERT: D 546 GLU cc_start: 0.8093 (mp0) cc_final: 0.7853 (mp0) REVERT: D 584 LEU cc_start: 0.8425 (mt) cc_final: 0.8194 (mm) REVERT: D 631 GLU cc_start: 0.7564 (pt0) cc_final: 0.7160 (mm-30) REVERT: D 682 GLU cc_start: 0.8065 (pt0) cc_final: 0.7656 (pp20) REVERT: D 693 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.7284 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 280 average time/residue: 0.5723 time to fit residues: 180.3906 Evaluate side-chains 284 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN B 430 HIS B 523 HIS C 430 HIS C 645 GLN A 430 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.215489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145628 restraints weight = 17246.931| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.94 r_work: 0.3523 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19173 Z= 0.126 Angle : 0.512 7.677 25991 Z= 0.268 Chirality : 0.037 0.149 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.856 163.980 2954 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.15 % Allowed : 21.97 % Favored : 76.88 % 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: 0.37 (0.17), residues: 2390 helix: 1.16 (0.13), residues: 1640 sheet: -1.48 (0.54), residues: 72 loop : -1.80 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 693 TYR 0.021 0.002 TYR D 451 PHE 0.013 0.001 PHE A 445 TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00286 (19172) covalent geometry : angle 0.51211 (25989) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.78153 ( 2) hydrogen bonds : bond 0.03617 ( 1137) hydrogen bonds : angle 4.20091 ( 3387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7010 (t0) cc_final: 0.6303 (p0) REVERT: B 320 MET cc_start: 0.8270 (tpp) cc_final: 0.8015 (tpp) REVERT: B 327 ARG cc_start: 0.6714 (tpp-160) cc_final: 0.6217 (ttm170) REVERT: B 340 ASP cc_start: 0.7650 (t70) cc_final: 0.7097 (t0) REVERT: B 371 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6148 (tpt170) REVERT: B 419 MET cc_start: 0.8270 (mtm) cc_final: 0.7736 (mtm) REVERT: B 426 HIS cc_start: 0.8217 (t70) cc_final: 0.7929 (t-90) REVERT: B 434 LYS cc_start: 0.8246 (mttt) cc_final: 0.7319 (ttpp) REVERT: B 488 MET cc_start: 0.7338 (mtm) cc_final: 0.6755 (mmm) REVERT: B 584 LEU cc_start: 0.8428 (mt) cc_final: 0.8188 (mm) REVERT: B 645 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7682 (mt0) REVERT: B 652 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 682 GLU cc_start: 0.8029 (pt0) cc_final: 0.7585 (pp20) REVERT: C 159 MET cc_start: 0.4984 (mmt) cc_final: 0.4695 (mmp) REVERT: C 340 ASP cc_start: 0.7585 (t70) cc_final: 0.7039 (t0) REVERT: C 371 ARG cc_start: 0.6444 (tpt170) cc_final: 0.6237 (tpt170) REVERT: C 419 MET cc_start: 0.8357 (mtm) cc_final: 0.7985 (mtm) REVERT: C 434 LYS cc_start: 0.8287 (mttt) cc_final: 0.7361 (ttpp) REVERT: C 488 MET cc_start: 0.7463 (mtm) cc_final: 0.6798 (mmm) REVERT: C 495 MET cc_start: 0.7799 (mtm) cc_final: 0.7386 (mtp) REVERT: C 546 GLU cc_start: 0.8110 (mp0) cc_final: 0.7832 (mp0) REVERT: C 682 GLU cc_start: 0.7894 (pt0) cc_final: 0.7460 (pp20) REVERT: C 693 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: A 179 ILE cc_start: 0.5023 (OUTLIER) cc_final: 0.4771 (pp) REVERT: A 340 ASP cc_start: 0.7661 (t70) cc_final: 0.7079 (t0) REVERT: A 419 MET cc_start: 0.8093 (mtm) cc_final: 0.7609 (mtm) REVERT: A 434 LYS cc_start: 0.8277 (mttt) cc_final: 0.7311 (ttpp) REVERT: A 495 MET cc_start: 0.7761 (mtm) cc_final: 0.7392 (mtp) REVERT: A 645 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7617 (mt0) REVERT: A 682 GLU cc_start: 0.8119 (pt0) cc_final: 0.7673 (pp20) REVERT: A 693 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.6935 (mtm110) REVERT: A 732 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7016 (tp) REVERT: D 330 ASN cc_start: 0.7266 (p0) cc_final: 0.7052 (p0) REVERT: D 340 ASP cc_start: 0.7683 (t70) cc_final: 0.7179 (t0) REVERT: D 426 HIS cc_start: 0.8169 (t70) cc_final: 0.7925 (t-90) REVERT: D 434 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7506 (mppt) REVERT: D 488 MET cc_start: 0.7165 (mtm) cc_final: 0.6656 (mmm) REVERT: D 540 TYR cc_start: 0.7684 (t80) cc_final: 0.7474 (t80) REVERT: D 546 GLU cc_start: 0.8092 (mp0) cc_final: 0.7844 (mp0) REVERT: D 584 LEU cc_start: 0.8415 (mt) cc_final: 0.8177 (mm) REVERT: D 631 GLU cc_start: 0.7605 (pt0) cc_final: 0.7155 (mm-30) REVERT: D 682 GLU cc_start: 0.8070 (pt0) cc_final: 0.7646 (pp20) REVERT: D 693 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7275 (ttm-80) outliers start: 20 outliers final: 15 residues processed: 280 average time/residue: 0.5552 time to fit residues: 175.2688 Evaluate side-chains 285 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 196 optimal weight: 0.1980 chunk 237 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 204 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN B 523 HIS C 430 HIS A 430 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.215717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150053 restraints weight = 17357.694| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.31 r_work: 0.3538 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19173 Z= 0.117 Angle : 0.514 8.074 25991 Z= 0.268 Chirality : 0.036 0.151 3061 Planarity : 0.004 0.055 3169 Dihedral : 11.720 163.907 2954 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.61 % Allowed : 21.62 % Favored : 76.77 % 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: 0.51 (0.17), residues: 2390 helix: 1.26 (0.13), residues: 1640 sheet: -1.42 (0.54), residues: 72 loop : -1.73 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.022 0.002 TYR B 451 PHE 0.013 0.001 PHE A 445 TRP 0.025 0.001 TRP B 380 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00259 (19172) covalent geometry : angle 0.51360 (25989) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.66881 ( 2) hydrogen bonds : bond 0.03544 ( 1137) hydrogen bonds : angle 4.15753 ( 3387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.7010 (t0) cc_final: 0.6313 (p0) REVERT: B 320 MET cc_start: 0.8305 (tpp) cc_final: 0.8048 (tpp) REVERT: B 327 ARG cc_start: 0.6711 (tpp-160) cc_final: 0.6279 (ttm170) REVERT: B 340 ASP cc_start: 0.7672 (t70) cc_final: 0.7126 (t0) REVERT: B 371 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6204 (tpt170) REVERT: B 419 MET cc_start: 0.8279 (mtm) cc_final: 0.7803 (mtm) REVERT: B 426 HIS cc_start: 0.8225 (t70) cc_final: 0.7952 (t-90) REVERT: B 434 LYS cc_start: 0.8277 (mttt) cc_final: 0.7357 (ttpp) REVERT: B 488 MET cc_start: 0.7330 (mtm) cc_final: 0.6762 (mmm) REVERT: B 584 LEU cc_start: 0.8442 (mt) cc_final: 0.8202 (mm) REVERT: B 645 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7702 (mt0) REVERT: B 652 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8410 (mm) REVERT: B 682 GLU cc_start: 0.8032 (pt0) cc_final: 0.7652 (pp20) REVERT: B 706 MET cc_start: 0.7999 (mtp) cc_final: 0.7661 (mtp) REVERT: C 159 MET cc_start: 0.4981 (mmt) cc_final: 0.4699 (mmp) REVERT: C 340 ASP cc_start: 0.7593 (t70) cc_final: 0.7080 (t0) REVERT: C 419 MET cc_start: 0.8335 (mtm) cc_final: 0.7971 (mtm) REVERT: C 434 LYS cc_start: 0.8292 (mttt) cc_final: 0.7384 (ttpp) REVERT: C 488 MET cc_start: 0.7477 (mtm) cc_final: 0.6826 (mmm) REVERT: C 495 MET cc_start: 0.7839 (mtm) cc_final: 0.7424 (mtp) REVERT: C 546 GLU cc_start: 0.8153 (mp0) cc_final: 0.7892 (mp0) REVERT: C 649 LYS cc_start: 0.8299 (ptpt) cc_final: 0.8044 (ptpt) REVERT: C 682 GLU cc_start: 0.7934 (pt0) cc_final: 0.7507 (pp20) REVERT: C 693 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7437 (ttp-110) REVERT: C 706 MET cc_start: 0.7778 (mtp) cc_final: 0.7533 (mtp) REVERT: A 179 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4846 (pp) REVERT: A 340 ASP cc_start: 0.7622 (t70) cc_final: 0.7084 (t0) REVERT: A 419 MET cc_start: 0.8127 (mtm) cc_final: 0.7673 (mtm) REVERT: A 434 LYS cc_start: 0.8305 (mttt) cc_final: 0.7346 (ttpp) REVERT: A 495 MET cc_start: 0.7799 (mtm) cc_final: 0.7433 (mtp) REVERT: A 645 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7597 (mt0) REVERT: A 682 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: A 693 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7008 (mtm110) REVERT: A 732 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7062 (tp) REVERT: D 340 ASP cc_start: 0.7591 (t70) cc_final: 0.7088 (t0) REVERT: D 426 HIS cc_start: 0.8201 (t70) cc_final: 0.7957 (t-90) REVERT: D 434 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7546 (mppt) REVERT: D 488 MET cc_start: 0.7163 (mtm) cc_final: 0.6665 (mmm) REVERT: D 540 TYR cc_start: 0.7710 (t80) cc_final: 0.7502 (t80) REVERT: D 546 GLU cc_start: 0.8105 (mp0) cc_final: 0.7858 (mp0) REVERT: D 584 LEU cc_start: 0.8432 (mt) cc_final: 0.8198 (mm) REVERT: D 631 GLU cc_start: 0.7580 (pt0) cc_final: 0.7111 (mm-30) REVERT: D 682 GLU cc_start: 0.8106 (pt0) cc_final: 0.7696 (pp20) REVERT: D 693 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7367 (ttm-80) REVERT: D 706 MET cc_start: 0.8013 (mtp) cc_final: 0.7686 (mtp) outliers start: 28 outliers final: 11 residues processed: 290 average time/residue: 0.5675 time to fit residues: 185.7864 Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.0170 chunk 226 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 63 optimal weight: 0.3980 chunk 2 optimal weight: 20.0000 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 HIS B 523 HIS C 330 ASN C 430 HIS A 430 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.215855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145243 restraints weight = 17285.536| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.66 r_work: 0.3524 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19173 Z= 0.116 Angle : 0.521 8.541 25991 Z= 0.271 Chirality : 0.036 0.147 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.679 163.830 2954 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.27 % Allowed : 21.85 % Favored : 76.88 % 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: 0.56 (0.17), residues: 2390 helix: 1.34 (0.13), residues: 1628 sheet: -1.40 (0.54), residues: 72 loop : -1.78 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 693 TYR 0.030 0.002 TYR A 208 PHE 0.017 0.001 PHE D 445 TRP 0.024 0.001 TRP B 380 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00253 (19172) covalent geometry : angle 0.52089 (25989) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.64425 ( 2) hydrogen bonds : bond 0.03521 ( 1137) hydrogen bonds : angle 4.14631 ( 3387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 ASP cc_start: 0.6998 (t0) cc_final: 0.6342 (p0) REVERT: B 320 MET cc_start: 0.8299 (tpp) cc_final: 0.8045 (tpp) REVERT: B 340 ASP cc_start: 0.7645 (t70) cc_final: 0.7109 (t0) REVERT: B 371 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6220 (tpt170) REVERT: B 419 MET cc_start: 0.8263 (mtm) cc_final: 0.7781 (mtm) REVERT: B 426 HIS cc_start: 0.8224 (t70) cc_final: 0.7928 (t-90) REVERT: B 434 LYS cc_start: 0.8241 (mttt) cc_final: 0.7328 (ttpp) REVERT: B 488 MET cc_start: 0.7362 (mtm) cc_final: 0.6812 (mmm) REVERT: B 584 LEU cc_start: 0.8436 (mt) cc_final: 0.8207 (mm) REVERT: B 645 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7744 (mt0) REVERT: B 652 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 682 GLU cc_start: 0.8000 (pt0) cc_final: 0.7640 (pp20) REVERT: B 693 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: C 159 MET cc_start: 0.5046 (mmt) cc_final: 0.4760 (mmp) REVERT: C 340 ASP cc_start: 0.7517 (t70) cc_final: 0.7012 (t0) REVERT: C 419 MET cc_start: 0.8334 (mtm) cc_final: 0.7969 (mtm) REVERT: C 434 LYS cc_start: 0.8247 (mttt) cc_final: 0.7352 (ttpp) REVERT: C 488 MET cc_start: 0.7496 (mtm) cc_final: 0.6868 (mmm) REVERT: C 495 MET cc_start: 0.7806 (mtm) cc_final: 0.7398 (mtp) REVERT: C 546 GLU cc_start: 0.8140 (mp0) cc_final: 0.7877 (mp0) REVERT: C 649 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8025 (ptpt) REVERT: C 682 GLU cc_start: 0.7899 (pt0) cc_final: 0.7499 (pp20) REVERT: C 693 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7400 (ttp-110) REVERT: C 706 MET cc_start: 0.7778 (mtp) cc_final: 0.7518 (mtp) REVERT: A 179 ILE cc_start: 0.5064 (OUTLIER) cc_final: 0.4847 (pp) REVERT: A 340 ASP cc_start: 0.7595 (t70) cc_final: 0.7077 (t0) REVERT: A 419 MET cc_start: 0.8121 (mtm) cc_final: 0.7669 (mtm) REVERT: A 434 LYS cc_start: 0.8272 (mttt) cc_final: 0.7324 (ttpp) REVERT: A 495 MET cc_start: 0.7780 (mtm) cc_final: 0.7419 (mtp) REVERT: A 645 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7626 (mt0) REVERT: A 682 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: A 693 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.6983 (mtm110) REVERT: A 732 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (tp) REVERT: D 340 ASP cc_start: 0.7564 (t70) cc_final: 0.7076 (t0) REVERT: D 426 HIS cc_start: 0.8166 (t70) cc_final: 0.7927 (t-90) REVERT: D 434 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7514 (mppt) REVERT: D 488 MET cc_start: 0.7156 (mtm) cc_final: 0.6678 (mmm) REVERT: D 540 TYR cc_start: 0.7682 (t80) cc_final: 0.7478 (t80) REVERT: D 546 GLU cc_start: 0.8094 (mp0) cc_final: 0.7851 (mp0) REVERT: D 584 LEU cc_start: 0.8423 (mt) cc_final: 0.8202 (mm) REVERT: D 631 GLU cc_start: 0.7482 (pt0) cc_final: 0.7098 (mm-30) REVERT: D 645 GLN cc_start: 0.8450 (tp40) cc_final: 0.7714 (mt0) REVERT: D 682 GLU cc_start: 0.8064 (pt0) cc_final: 0.7670 (pp20) REVERT: D 706 MET cc_start: 0.8002 (mtp) cc_final: 0.7679 (mtp) outliers start: 22 outliers final: 10 residues processed: 289 average time/residue: 0.5711 time to fit residues: 185.9256 Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 0.0870 chunk 163 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 150 optimal weight: 0.0980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 HIS B 523 HIS C 430 HIS A 430 HIS ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.215947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149798 restraints weight = 17339.155| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.05 r_work: 0.3518 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19173 Z= 0.116 Angle : 0.521 8.541 25991 Z= 0.271 Chirality : 0.036 0.147 3061 Planarity : 0.004 0.056 3169 Dihedral : 11.679 163.830 2954 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.92 % Allowed : 22.31 % Favored : 76.77 % 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: 0.56 (0.17), residues: 2390 helix: 1.34 (0.13), residues: 1628 sheet: -1.40 (0.54), residues: 72 loop : -1.78 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 693 TYR 0.030 0.002 TYR A 208 PHE 0.017 0.001 PHE D 445 TRP 0.024 0.001 TRP B 380 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00253 (19172) covalent geometry : angle 0.52089 (25989) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.64425 ( 2) hydrogen bonds : bond 0.03521 ( 1137) hydrogen bonds : angle 4.14631 ( 3387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8264.60 seconds wall clock time: 141 minutes 48.85 seconds (8508.85 seconds total)