Starting phenix.real_space_refine on Thu Feb 5 02:58:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc8_42117/02_2026/8uc8_42117_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9720 2.51 5 N 2460 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14804 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 174 Chain: "C" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 174 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 174 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 4.09, per 1000 atoms: 0.28 Number of scatterers: 14804 At special positions: 0 Unit cell: (121.656, 121.656, 112.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2516 8.00 N 2460 7.00 C 9720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 725.5 milliseconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 70.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 removed outlier: 4.093A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 584 Processing helix chain 'C' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 194 removed outlier: 4.076A pdb=" N PHE C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.019A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.719A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.767A pdb=" N SER B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.021A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 584 Processing sheet with id=AA1, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.588A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.483A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 3015 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: 2.85 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2276 1.27 - 1.41: 3900 1.41 - 1.54: 8520 1.54 - 1.68: 268 1.68 - 1.82: 188 Bond restraints: 15152 Sorted by residual: bond pdb=" C ARG C 404 " pdb=" O ARG C 404 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.22e-02 6.72e+03 6.29e+01 bond pdb=" C ARG A 404 " pdb=" O ARG A 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.26e+01 bond pdb=" C ARG B 404 " pdb=" O ARG B 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.22e+01 bond pdb=" C ARG D 404 " pdb=" O ARG D 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.17e+01 bond pdb=" C11 PCW C 902 " pdb=" O3 PCW C 902 " ideal model delta sigma weight residual 1.326 1.466 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 20359 5.18 - 10.35: 133 10.35 - 15.53: 8 15.53 - 20.70: 8 20.70 - 25.88: 4 Bond angle restraints: 20512 Sorted by residual: angle pdb=" C19 PCW A 705 " pdb=" C20 PCW A 705 " pdb=" C21 PCW A 705 " ideal model delta sigma weight residual 127.82 153.70 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C19 PCW B 901 " pdb=" C20 PCW B 901 " pdb=" C21 PCW B 901 " ideal model delta sigma weight residual 127.82 153.70 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " pdb=" C21 PCW A 704 " ideal model delta sigma weight residual 127.82 153.69 -25.87 3.00e+00 1.11e-01 7.43e+01 angle pdb=" C19 PCW C 901 " pdb=" C20 PCW C 901 " pdb=" C21 PCW C 901 " ideal model delta sigma weight residual 127.82 153.67 -25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" C38 PCW B 902 " pdb=" C39 PCW B 902 " pdb=" C40 PCW B 902 " ideal model delta sigma weight residual 127.57 148.22 -20.65 3.00e+00 1.11e-01 4.74e+01 ... (remaining 20507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 8736 35.48 - 70.96: 164 70.96 - 106.45: 12 106.45 - 141.93: 0 141.93 - 177.41: 4 Dihedral angle restraints: 8916 sinusoidal: 3212 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR C 361 " pdb=" C TYR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 361 " pdb=" C TYR B 361 " pdb=" N GLY B 362 " pdb=" CA GLY B 362 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 8913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1464 0.075 - 0.150: 601 0.150 - 0.225: 167 0.225 - 0.300: 36 0.300 - 0.375: 8 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA TRP C 281 " pdb=" N TRP C 281 " pdb=" C TRP C 281 " pdb=" CB TRP C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA TRP A 281 " pdb=" N TRP A 281 " pdb=" C TRP A 281 " pdb=" CB TRP A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TRP D 281 " pdb=" N TRP D 281 " pdb=" C TRP D 281 " pdb=" CB TRP D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 2273 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " 0.184 2.00e-02 2.50e+03 8.90e-02 1.98e+02 pdb=" CG TRP C 281 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " 0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.184 2.00e-02 2.50e+03 8.89e-02 1.98e+02 pdb=" CG TRP A 281 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 281 " 0.184 2.00e-02 2.50e+03 8.89e-02 1.98e+02 pdb=" CG TRP D 281 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 281 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP D 281 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP D 281 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP D 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 281 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 281 " 0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 281 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP D 281 " 0.079 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 417 2.74 - 3.28: 15831 3.28 - 3.82: 24744 3.82 - 4.36: 31799 4.36 - 4.90: 53479 Nonbonded interactions: 126270 Sorted by model distance: nonbonded pdb=" NH1 ARG B 142 " pdb=" OD1 ASP B 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG D 142 " pdb=" OD1 ASP D 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG C 142 " pdb=" OD1 ASP C 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG A 142 " pdb=" OD1 ASP A 146 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG C 438 " pdb=" OE2 GLU C 446 " model vdw 2.257 3.120 ... (remaining 126265 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 94 through 586 or (resid 701 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 702 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 703 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'B' and (resid 94 through 586 or (resid 901 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 902 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 903 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'C' and (resid 94 through 586 or (resid 901 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 902 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 903 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'D' and (resid 94 through 586 or (resid 701 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 702 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 703 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 0.013 0.140 15152 Z= 0.760 Angle : 1.840 25.880 20512 Z= 1.194 Chirality : 0.089 0.375 2276 Planarity : 0.014 0.089 2604 Dihedral : 15.096 177.408 5228 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.60 % Allowed : 3.87 % Favored : 95.54 % 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: -1.40 (0.18), residues: 1920 helix: -1.21 (0.12), residues: 1288 sheet: 0.84 (0.75), residues: 48 loop : 0.14 (0.29), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 270 TYR 0.110 0.022 TYR A 439 PHE 0.062 0.011 PHE B 109 TRP 0.184 0.035 TRP C 281 HIS 0.015 0.005 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.01297 (15152) covalent geometry : angle 1.83982 (20512) hydrogen bonds : bond 0.15155 ( 1017) hydrogen bonds : angle 7.74209 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 344 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.7185 (tptp) cc_final: 0.6708 (tttt) REVERT: D 140 ASP cc_start: 0.6825 (m-30) cc_final: 0.6568 (m-30) REVERT: D 152 MET cc_start: 0.7554 (tpp) cc_final: 0.7291 (tpt) REVERT: D 283 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5692 (mm-30) REVERT: D 305 MET cc_start: 0.7991 (mtp) cc_final: 0.7608 (mtp) REVERT: D 369 MET cc_start: 0.8138 (ttt) cc_final: 0.7938 (ttm) REVERT: D 371 ASP cc_start: 0.7361 (t0) cc_final: 0.6801 (m-30) REVERT: D 379 MET cc_start: 0.8677 (mtp) cc_final: 0.8357 (mtm) REVERT: D 388 MET cc_start: 0.8237 (tpp) cc_final: 0.7890 (mmm) REVERT: D 412 LYS cc_start: 0.7240 (mttp) cc_final: 0.6995 (mtmm) REVERT: D 429 GLN cc_start: 0.7091 (tp40) cc_final: 0.6627 (tp40) REVERT: D 433 ASP cc_start: 0.7418 (m-30) cc_final: 0.6909 (m-30) REVERT: D 446 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6774 (tt0) REVERT: D 448 ASN cc_start: 0.6817 (t0) cc_final: 0.6258 (m-40) REVERT: D 459 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6762 (tt0) REVERT: D 460 GLU cc_start: 0.7748 (tt0) cc_final: 0.7513 (pt0) REVERT: D 482 ASN cc_start: 0.6463 (p0) cc_final: 0.5994 (t0) REVERT: D 492 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6970 (mmp80) REVERT: C 118 LYS cc_start: 0.7182 (tptp) cc_final: 0.6729 (tttt) REVERT: C 140 ASP cc_start: 0.6821 (m-30) cc_final: 0.6558 (m-30) REVERT: C 152 MET cc_start: 0.7552 (tpp) cc_final: 0.7349 (tpt) REVERT: C 283 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5784 (mm-30) REVERT: C 305 MET cc_start: 0.8006 (mtp) cc_final: 0.7638 (mtp) REVERT: C 371 ASP cc_start: 0.7355 (t0) cc_final: 0.6793 (m-30) REVERT: C 412 LYS cc_start: 0.7274 (mttp) cc_final: 0.7023 (mtmm) REVERT: C 429 GLN cc_start: 0.7106 (tp40) cc_final: 0.6421 (tp-100) REVERT: C 433 ASP cc_start: 0.7405 (m-30) cc_final: 0.6782 (m-30) REVERT: C 446 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6797 (tt0) REVERT: C 448 ASN cc_start: 0.6861 (t0) cc_final: 0.6306 (m-40) REVERT: C 459 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6758 (tt0) REVERT: C 460 GLU cc_start: 0.7759 (tt0) cc_final: 0.7517 (pt0) REVERT: C 482 ASN cc_start: 0.6433 (p0) cc_final: 0.5998 (t0) REVERT: C 492 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.6981 (mmp80) REVERT: A 118 LYS cc_start: 0.7179 (tptp) cc_final: 0.6707 (tttt) REVERT: A 140 ASP cc_start: 0.6840 (m-30) cc_final: 0.6573 (m-30) REVERT: A 152 MET cc_start: 0.7557 (tpp) cc_final: 0.7334 (tpt) REVERT: A 283 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5671 (mm-30) REVERT: A 305 MET cc_start: 0.7947 (mtp) cc_final: 0.7565 (mtp) REVERT: A 369 MET cc_start: 0.8229 (ttt) cc_final: 0.8006 (ttm) REVERT: A 371 ASP cc_start: 0.7335 (t0) cc_final: 0.6791 (m-30) REVERT: A 388 MET cc_start: 0.8230 (tpp) cc_final: 0.7856 (mmm) REVERT: A 412 LYS cc_start: 0.7235 (mttp) cc_final: 0.7007 (mtmm) REVERT: A 429 GLN cc_start: 0.7067 (tp40) cc_final: 0.6628 (tp40) REVERT: A 433 ASP cc_start: 0.7327 (m-30) cc_final: 0.6880 (m-30) REVERT: A 446 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6809 (tt0) REVERT: A 448 ASN cc_start: 0.6857 (t0) cc_final: 0.6273 (m-40) REVERT: A 459 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6748 (tt0) REVERT: A 482 ASN cc_start: 0.6382 (p0) cc_final: 0.5966 (t0) REVERT: B 118 LYS cc_start: 0.7202 (tptp) cc_final: 0.6753 (tttt) REVERT: B 140 ASP cc_start: 0.6831 (m-30) cc_final: 0.6562 (m-30) REVERT: B 152 MET cc_start: 0.7532 (tpp) cc_final: 0.7320 (tpt) REVERT: B 283 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5767 (mm-30) REVERT: B 305 MET cc_start: 0.7969 (mtp) cc_final: 0.7595 (mtp) REVERT: B 371 ASP cc_start: 0.7339 (t0) cc_final: 0.6778 (m-30) REVERT: B 388 MET cc_start: 0.8187 (tpp) cc_final: 0.7839 (mmm) REVERT: B 412 LYS cc_start: 0.7279 (mttp) cc_final: 0.7024 (mtmm) REVERT: B 429 GLN cc_start: 0.7095 (tp40) cc_final: 0.6612 (tp40) REVERT: B 433 ASP cc_start: 0.7386 (m-30) cc_final: 0.6954 (m-30) REVERT: B 446 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6770 (tt0) REVERT: B 448 ASN cc_start: 0.6870 (t0) cc_final: 0.6278 (m-40) REVERT: B 459 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6761 (tt0) REVERT: B 460 GLU cc_start: 0.7789 (tt0) cc_final: 0.7579 (pt0) REVERT: B 482 ASN cc_start: 0.6358 (p0) cc_final: 0.5974 (t0) REVERT: B 492 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6981 (mmp80) outliers start: 8 outliers final: 7 residues processed: 352 average time/residue: 0.5302 time to fit residues: 205.7458 Evaluate side-chains 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 404 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN D 323 GLN C 103 GLN C 323 GLN A 103 GLN A 323 GLN A 416 GLN B 103 GLN B 323 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151656 restraints weight = 15827.053| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 0.87 r_work: 0.3647 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.160 Angle : 0.562 5.625 20512 Z= 0.307 Chirality : 0.043 0.153 2276 Planarity : 0.005 0.049 2604 Dihedral : 12.616 156.891 2320 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.68 % Allowed : 10.49 % Favored : 86.83 % 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 (0.19), residues: 1920 helix: 0.41 (0.14), residues: 1312 sheet: 1.51 (0.75), residues: 48 loop : 0.56 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 405 TYR 0.022 0.002 TYR A 411 PHE 0.015 0.001 PHE D 143 TRP 0.024 0.002 TRP D 281 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00344 (15152) covalent geometry : angle 0.56185 (20512) hydrogen bonds : bond 0.04815 ( 1017) hydrogen bonds : angle 5.24284 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.552 Fit side-chains REVERT: D 118 LYS cc_start: 0.7976 (tptp) cc_final: 0.7761 (tttt) REVERT: D 184 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7685 (p) REVERT: D 258 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6399 (ttt180) REVERT: C 118 LYS cc_start: 0.7999 (tptp) cc_final: 0.7773 (tttt) REVERT: C 184 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7697 (p) REVERT: C 258 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6390 (ttt180) REVERT: A 118 LYS cc_start: 0.7980 (tptp) cc_final: 0.7772 (tttt) REVERT: A 184 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 258 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6420 (ttt180) REVERT: A 460 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: A 492 ARG cc_start: 0.8597 (mmp80) cc_final: 0.8209 (mmp80) REVERT: B 118 LYS cc_start: 0.7987 (tptp) cc_final: 0.7787 (tttt) REVERT: B 184 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 258 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6418 (ttt180) outliers start: 36 outliers final: 9 residues processed: 281 average time/residue: 0.5067 time to fit residues: 157.4761 Evaluate side-chains 221 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143754 restraints weight = 16352.566| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 0.83 r_work: 0.3562 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15152 Z= 0.253 Angle : 0.613 7.141 20512 Z= 0.323 Chirality : 0.044 0.140 2276 Planarity : 0.005 0.046 2604 Dihedral : 11.211 134.154 2292 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.53 % Allowed : 13.32 % Favored : 84.15 % 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 (0.18), residues: 1920 helix: 0.41 (0.14), residues: 1320 sheet: 0.93 (0.74), residues: 48 loop : 0.05 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 492 TYR 0.025 0.002 TYR B 411 PHE 0.020 0.002 PHE D 143 TRP 0.022 0.002 TRP C 281 HIS 0.006 0.002 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00581 (15152) covalent geometry : angle 0.61296 (20512) hydrogen bonds : bond 0.04882 ( 1017) hydrogen bonds : angle 5.20298 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.612 Fit side-chains REVERT: D 113 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7802 (tpp) REVERT: D 118 LYS cc_start: 0.8024 (tptp) cc_final: 0.7746 (tttt) REVERT: D 287 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6591 (mmt) REVERT: D 482 ASN cc_start: 0.6701 (t0) cc_final: 0.6086 (t0) REVERT: C 118 LYS cc_start: 0.8036 (tptp) cc_final: 0.7764 (tttt) REVERT: C 283 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7058 (mm-30) REVERT: C 482 ASN cc_start: 0.6720 (t0) cc_final: 0.6155 (t0) REVERT: A 113 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7760 (tpp) REVERT: A 118 LYS cc_start: 0.8031 (tptp) cc_final: 0.7760 (tttt) REVERT: A 283 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7105 (mm-30) REVERT: A 287 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6533 (mmt) REVERT: A 482 ASN cc_start: 0.6610 (t0) cc_final: 0.6016 (t0) REVERT: B 118 LYS cc_start: 0.8026 (tptp) cc_final: 0.7773 (tttt) REVERT: B 283 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7044 (mm-30) REVERT: B 287 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6542 (mmt) REVERT: B 452 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8136 (mt-10) REVERT: B 482 ASN cc_start: 0.6671 (t0) cc_final: 0.6098 (t0) outliers start: 34 outliers final: 7 residues processed: 223 average time/residue: 0.5156 time to fit residues: 126.7380 Evaluate side-chains 201 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 160 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 408 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS A 408 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148145 restraints weight = 16205.335| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.96 r_work: 0.3571 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.142 Angle : 0.502 5.208 20512 Z= 0.267 Chirality : 0.040 0.125 2276 Planarity : 0.004 0.041 2604 Dihedral : 10.225 113.217 2292 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.05 % Allowed : 14.51 % Favored : 82.44 % 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: 0.84 (0.19), residues: 1920 helix: 0.86 (0.14), residues: 1308 sheet: 0.63 (0.70), residues: 48 loop : 0.11 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 492 TYR 0.022 0.002 TYR C 411 PHE 0.015 0.001 PHE C 236 TRP 0.022 0.002 TRP D 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00311 (15152) covalent geometry : angle 0.50241 (20512) hydrogen bonds : bond 0.04171 ( 1017) hydrogen bonds : angle 4.85764 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.475 Fit side-chains REVERT: D 118 LYS cc_start: 0.8136 (tptp) cc_final: 0.7745 (tttt) REVERT: D 258 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6222 (ttt180) REVERT: D 283 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7123 (mm-30) REVERT: C 118 LYS cc_start: 0.8117 (tptp) cc_final: 0.7714 (tttt) REVERT: C 258 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6241 (ttt180) REVERT: C 283 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7069 (mm-30) REVERT: C 287 MET cc_start: 0.7250 (mmt) cc_final: 0.6493 (mmt) REVERT: A 118 LYS cc_start: 0.8121 (tptp) cc_final: 0.7724 (tttt) REVERT: A 258 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6221 (ttt180) REVERT: A 283 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7091 (mm-30) REVERT: A 452 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 118 LYS cc_start: 0.8124 (tptp) cc_final: 0.7713 (tttt) REVERT: B 192 MET cc_start: 0.7520 (mpt) cc_final: 0.7317 (mpt) REVERT: B 258 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6223 (ttt180) REVERT: B 283 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 452 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8192 (mt-10) outliers start: 41 outliers final: 11 residues processed: 229 average time/residue: 0.4610 time to fit residues: 118.1555 Evaluate side-chains 207 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 HIS D 355 HIS D 482 ASN C 279 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN C 482 ASN A 279 HIS A 355 HIS A 482 ASN B 279 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144497 restraints weight = 16224.356| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 0.87 r_work: 0.3535 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15152 Z= 0.212 Angle : 0.550 6.396 20512 Z= 0.288 Chirality : 0.042 0.129 2276 Planarity : 0.004 0.040 2604 Dihedral : 9.979 103.419 2292 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.68 % Allowed : 15.92 % Favored : 81.40 % 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: 0.79 (0.19), residues: 1920 helix: 0.89 (0.14), residues: 1304 sheet: 0.40 (0.68), residues: 48 loop : -0.08 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 267 TYR 0.024 0.002 TYR C 411 PHE 0.015 0.002 PHE C 141 TRP 0.021 0.002 TRP B 281 HIS 0.006 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00486 (15152) covalent geometry : angle 0.55038 (20512) hydrogen bonds : bond 0.04338 ( 1017) hydrogen bonds : angle 4.91969 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.615 Fit side-chains REVERT: D 118 LYS cc_start: 0.8117 (tptp) cc_final: 0.7664 (tttt) REVERT: D 258 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6225 (ttt180) REVERT: D 287 MET cc_start: 0.7286 (mmt) cc_final: 0.6512 (mmt) REVERT: D 482 ASN cc_start: 0.6883 (t0) cc_final: 0.6298 (t0) REVERT: C 118 LYS cc_start: 0.8096 (tptp) cc_final: 0.7656 (tttt) REVERT: C 238 ILE cc_start: 0.7534 (mm) cc_final: 0.7333 (mm) REVERT: C 258 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6240 (ttt180) REVERT: C 287 MET cc_start: 0.7277 (mmt) cc_final: 0.6496 (mmt) REVERT: C 482 ASN cc_start: 0.6833 (t0) cc_final: 0.6297 (t0) REVERT: A 118 LYS cc_start: 0.8106 (tptp) cc_final: 0.7678 (tttt) REVERT: A 258 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6198 (ttt180) REVERT: A 283 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7203 (mm-30) REVERT: A 287 MET cc_start: 0.7259 (mmt) cc_final: 0.6486 (mmt) REVERT: A 482 ASN cc_start: 0.6784 (t0) cc_final: 0.6236 (t0) REVERT: B 118 LYS cc_start: 0.8078 (tptp) cc_final: 0.7651 (tttt) REVERT: B 258 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6226 (ttt180) REVERT: B 287 MET cc_start: 0.7252 (mmt) cc_final: 0.6465 (mmt) REVERT: B 482 ASN cc_start: 0.6844 (t0) cc_final: 0.6319 (t0) outliers start: 36 outliers final: 15 residues processed: 210 average time/residue: 0.5154 time to fit residues: 120.5262 Evaluate side-chains 199 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146145 restraints weight = 16064.715| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 0.86 r_work: 0.3541 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15152 Z= 0.169 Angle : 0.519 5.372 20512 Z= 0.271 Chirality : 0.041 0.131 2276 Planarity : 0.004 0.041 2604 Dihedral : 9.566 91.470 2292 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 16.52 % Favored : 81.25 % 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: 0.98 (0.19), residues: 1920 helix: 1.03 (0.14), residues: 1304 sheet: 0.44 (0.66), residues: 48 loop : 0.00 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 554 TYR 0.023 0.002 TYR C 411 PHE 0.015 0.001 PHE D 236 TRP 0.021 0.002 TRP A 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00384 (15152) covalent geometry : angle 0.51879 (20512) hydrogen bonds : bond 0.04109 ( 1017) hydrogen bonds : angle 4.80188 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.549 Fit side-chains REVERT: D 113 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: D 118 LYS cc_start: 0.8153 (tptp) cc_final: 0.7641 (tttt) REVERT: D 258 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6175 (ttt180) REVERT: D 287 MET cc_start: 0.7225 (mmt) cc_final: 0.6431 (mmt) REVERT: C 118 LYS cc_start: 0.8115 (tptp) cc_final: 0.7625 (tttt) REVERT: C 258 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6196 (ttt180) REVERT: C 287 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6394 (mmt) REVERT: A 118 LYS cc_start: 0.8129 (tptp) cc_final: 0.7624 (tttt) REVERT: A 258 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6142 (ttt180) REVERT: A 287 MET cc_start: 0.7218 (mmt) cc_final: 0.6424 (mmt) REVERT: B 118 LYS cc_start: 0.8111 (tptp) cc_final: 0.7623 (tttt) REVERT: B 141 PHE cc_start: 0.7810 (t80) cc_final: 0.7516 (t80) REVERT: B 258 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6163 (ttt180) REVERT: B 283 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7089 (mm-30) REVERT: B 287 MET cc_start: 0.7226 (mmt) cc_final: 0.6430 (mmt) REVERT: B 452 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8263 (mt-10) outliers start: 30 outliers final: 17 residues processed: 210 average time/residue: 0.5115 time to fit residues: 119.4323 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148090 restraints weight = 16022.143| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 0.92 r_work: 0.3576 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.145 Angle : 0.498 4.953 20512 Z= 0.261 Chirality : 0.040 0.120 2276 Planarity : 0.004 0.041 2604 Dihedral : 9.161 79.763 2292 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.68 % Allowed : 16.67 % Favored : 80.65 % 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: 1.22 (0.19), residues: 1920 helix: 1.18 (0.14), residues: 1312 sheet: 0.52 (0.61), residues: 68 loop : 0.15 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 492 TYR 0.021 0.002 TYR B 411 PHE 0.015 0.001 PHE C 236 TRP 0.020 0.002 TRP C 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00324 (15152) covalent geometry : angle 0.49842 (20512) hydrogen bonds : bond 0.03951 ( 1017) hydrogen bonds : angle 4.67439 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.564 Fit side-chains REVERT: D 118 LYS cc_start: 0.8121 (tptp) cc_final: 0.7680 (tttt) REVERT: D 141 PHE cc_start: 0.7649 (t80) cc_final: 0.7429 (t80) REVERT: D 232 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7795 (t) REVERT: D 238 ILE cc_start: 0.7418 (mp) cc_final: 0.7110 (mm) REVERT: D 258 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6178 (ttt180) REVERT: D 287 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6390 (mmt) REVERT: C 118 LYS cc_start: 0.8075 (tptp) cc_final: 0.7556 (tttt) REVERT: C 141 PHE cc_start: 0.7641 (t80) cc_final: 0.7424 (t80) REVERT: C 232 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7765 (t) REVERT: C 258 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6191 (ttt180) REVERT: C 287 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6390 (mmt) REVERT: A 113 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7721 (tpp) REVERT: A 118 LYS cc_start: 0.8090 (tptp) cc_final: 0.7654 (tttt) REVERT: A 141 PHE cc_start: 0.7641 (t80) cc_final: 0.7431 (t80) REVERT: A 232 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7786 (t) REVERT: A 258 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6134 (ttt180) REVERT: A 287 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6394 (mmt) REVERT: A 452 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 118 LYS cc_start: 0.8037 (tptp) cc_final: 0.7538 (tttt) REVERT: B 141 PHE cc_start: 0.7638 (t80) cc_final: 0.7412 (t80) REVERT: B 232 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 258 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6159 (ttt180) REVERT: B 287 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6375 (mmt) REVERT: B 452 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8265 (mt-10) outliers start: 36 outliers final: 12 residues processed: 216 average time/residue: 0.4564 time to fit residues: 110.2992 Evaluate side-chains 211 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 118 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151570 restraints weight = 16035.345| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 0.70 r_work: 0.3625 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.128 Angle : 0.493 6.050 20512 Z= 0.258 Chirality : 0.040 0.121 2276 Planarity : 0.004 0.040 2604 Dihedral : 8.904 70.442 2292 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.53 % Allowed : 17.56 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1920 helix: 1.31 (0.14), residues: 1316 sheet: 0.61 (0.60), residues: 68 loop : 0.31 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 554 TYR 0.020 0.001 TYR B 411 PHE 0.017 0.001 PHE A 236 TRP 0.019 0.002 TRP B 281 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00281 (15152) covalent geometry : angle 0.49322 (20512) hydrogen bonds : bond 0.03795 ( 1017) hydrogen bonds : angle 4.57237 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.565 Fit side-chains REVERT: D 113 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: D 118 LYS cc_start: 0.8091 (tptp) cc_final: 0.7604 (tttt) REVERT: D 141 PHE cc_start: 0.7516 (t80) cc_final: 0.7277 (t80) REVERT: D 192 MET cc_start: 0.7559 (mpt) cc_final: 0.7162 (mpt) REVERT: D 238 ILE cc_start: 0.7431 (mp) cc_final: 0.7078 (mm) REVERT: D 258 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6143 (ttt180) REVERT: D 287 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6356 (mmt) REVERT: C 118 LYS cc_start: 0.8098 (tptp) cc_final: 0.7581 (tttt) REVERT: C 141 PHE cc_start: 0.7478 (t80) cc_final: 0.7253 (t80) REVERT: C 192 MET cc_start: 0.7521 (mpt) cc_final: 0.7126 (mpt) REVERT: C 238 ILE cc_start: 0.7405 (mp) cc_final: 0.7087 (mm) REVERT: C 258 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6153 (ttt180) REVERT: C 287 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6356 (mmt) REVERT: A 113 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: A 118 LYS cc_start: 0.8090 (tptp) cc_final: 0.7595 (tttt) REVERT: A 141 PHE cc_start: 0.7519 (t80) cc_final: 0.7290 (t80) REVERT: A 192 MET cc_start: 0.7557 (mpt) cc_final: 0.7171 (mpt) REVERT: A 258 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6100 (ttt180) REVERT: A 287 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6373 (mmt) REVERT: B 118 LYS cc_start: 0.8046 (tptp) cc_final: 0.7567 (tttt) REVERT: B 141 PHE cc_start: 0.7474 (t80) cc_final: 0.7249 (t80) REVERT: B 192 MET cc_start: 0.7474 (mpt) cc_final: 0.7084 (mpt) REVERT: B 258 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6110 (ttt180) REVERT: B 283 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6958 (mm-30) REVERT: B 287 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6322 (mmt) REVERT: B 452 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8185 (mt-10) outliers start: 34 outliers final: 12 residues processed: 224 average time/residue: 0.4917 time to fit residues: 122.9610 Evaluate side-chains 215 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN A 429 GLN A 482 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149385 restraints weight = 16129.926| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 0.87 r_work: 0.3582 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15152 Z= 0.133 Angle : 0.508 7.500 20512 Z= 0.263 Chirality : 0.040 0.128 2276 Planarity : 0.004 0.041 2604 Dihedral : 8.807 59.790 2292 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.08 % Allowed : 18.30 % Favored : 79.61 % 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: 1.49 (0.20), residues: 1920 helix: 1.35 (0.15), residues: 1316 sheet: 0.60 (0.60), residues: 68 loop : 0.35 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 554 TYR 0.019 0.001 TYR B 411 PHE 0.016 0.001 PHE C 236 TRP 0.020 0.002 TRP A 281 HIS 0.005 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00293 (15152) covalent geometry : angle 0.50805 (20512) hydrogen bonds : bond 0.03753 ( 1017) hydrogen bonds : angle 4.53645 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.374 Fit side-chains REVERT: D 113 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7759 (tpp) REVERT: D 118 LYS cc_start: 0.8114 (tptp) cc_final: 0.7588 (tttt) REVERT: D 141 PHE cc_start: 0.7457 (t80) cc_final: 0.7202 (t80) REVERT: D 192 MET cc_start: 0.7584 (mpt) cc_final: 0.7214 (mpt) REVERT: D 258 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6154 (ttt180) REVERT: D 283 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7034 (mm-30) REVERT: C 118 LYS cc_start: 0.8099 (tptp) cc_final: 0.7576 (tttt) REVERT: C 141 PHE cc_start: 0.7462 (t80) cc_final: 0.7212 (t80) REVERT: C 238 ILE cc_start: 0.7384 (mp) cc_final: 0.7056 (mm) REVERT: C 258 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6153 (ttt180) REVERT: C 283 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7001 (mm-30) REVERT: C 287 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6365 (mmt) REVERT: A 113 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7728 (tpp) REVERT: A 118 LYS cc_start: 0.8067 (tptp) cc_final: 0.7562 (tttt) REVERT: A 141 PHE cc_start: 0.7446 (t80) cc_final: 0.7194 (t80) REVERT: A 192 MET cc_start: 0.7601 (mpt) cc_final: 0.7248 (mpt) REVERT: A 258 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6091 (ttt180) REVERT: A 283 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7162 (pt0) REVERT: B 118 LYS cc_start: 0.8069 (tptp) cc_final: 0.7539 (tttt) REVERT: B 141 PHE cc_start: 0.7433 (t80) cc_final: 0.7192 (t80) REVERT: B 192 MET cc_start: 0.7568 (mpt) cc_final: 0.7215 (mpt) REVERT: B 258 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6134 (ttt180) REVERT: B 283 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7012 (mm-30) REVERT: B 452 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8237 (mt-10) outliers start: 28 outliers final: 10 residues processed: 214 average time/residue: 0.4534 time to fit residues: 107.9317 Evaluate side-chains 214 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 0.0030 chunk 137 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.165587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149665 restraints weight = 16032.926| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.10 r_work: 0.3601 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.124 Angle : 0.506 8.935 20512 Z= 0.260 Chirality : 0.040 0.118 2276 Planarity : 0.004 0.041 2604 Dihedral : 8.286 59.995 2292 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.64 % Allowed : 18.38 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1920 helix: 1.38 (0.15), residues: 1320 sheet: 0.55 (0.61), residues: 48 loop : 0.36 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 554 TYR 0.019 0.001 TYR D 411 PHE 0.018 0.001 PHE D 236 TRP 0.019 0.002 TRP D 281 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00272 (15152) covalent geometry : angle 0.50614 (20512) hydrogen bonds : bond 0.03647 ( 1017) hydrogen bonds : angle 4.48299 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.597 Fit side-chains REVERT: D 113 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7791 (tpp) REVERT: D 118 LYS cc_start: 0.8101 (tptp) cc_final: 0.7549 (tttt) REVERT: D 141 PHE cc_start: 0.7442 (t80) cc_final: 0.7228 (t80) REVERT: D 192 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7163 (mpt) REVERT: D 258 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6070 (ttt180) REVERT: C 118 LYS cc_start: 0.8100 (tptp) cc_final: 0.7550 (tttt) REVERT: C 141 PHE cc_start: 0.7435 (t80) cc_final: 0.7229 (t80) REVERT: C 258 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6100 (ttt180) REVERT: A 113 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7753 (tpp) REVERT: A 118 LYS cc_start: 0.8085 (tptp) cc_final: 0.7531 (tttt) REVERT: A 141 PHE cc_start: 0.7446 (t80) cc_final: 0.7225 (t80) REVERT: A 192 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7234 (mpt) REVERT: A 258 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6079 (ttt180) REVERT: B 118 LYS cc_start: 0.8074 (tptp) cc_final: 0.7557 (tttt) REVERT: B 192 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7189 (mpt) REVERT: B 258 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6082 (ttt180) REVERT: B 452 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8230 (mt-10) outliers start: 22 outliers final: 6 residues processed: 215 average time/residue: 0.5008 time to fit residues: 119.8002 Evaluate side-chains 209 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 258 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151003 restraints weight = 16118.208| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 0.95 r_work: 0.3654 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.130 Angle : 0.519 9.211 20512 Z= 0.268 Chirality : 0.040 0.125 2276 Planarity : 0.004 0.040 2604 Dihedral : 7.944 59.889 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.56 % Allowed : 18.97 % Favored : 79.46 % 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: 1.53 (0.20), residues: 1920 helix: 1.39 (0.14), residues: 1320 sheet: 0.50 (0.62), residues: 48 loop : 0.35 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 554 TYR 0.019 0.001 TYR B 411 PHE 0.027 0.001 PHE B 236 TRP 0.027 0.002 TRP B 281 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00287 (15152) covalent geometry : angle 0.51928 (20512) hydrogen bonds : bond 0.03670 ( 1017) hydrogen bonds : angle 4.46887 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4286.86 seconds wall clock time: 74 minutes 3.71 seconds (4443.71 seconds total)