Starting phenix.real_space_refine on Thu Feb 5 17:24:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.map" model { file = "/net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qce_53010/02_2026/9qce_53010.cif" } resolution = 2.8 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= 1.164 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 29 5.16 5 C 11933 2.51 5 N 3058 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 18572 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4366 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 544} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'GLU:plan': 13, 'ARG:plan': 3, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4667 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 564} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 4418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4418 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 4, 'ASP:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1058 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2028 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 6, 'TRANS': 265} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 11, 'ASP:plan': 9, 'ARG:plan': 3, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 145 Chain: "F" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2035 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 267} Chain breaks: 6 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 12, 'ASP:plan': 7, 'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 125 Time building chain proxies: 4.09, per 1000 atoms: 0.22 Number of scatterers: 18572 At special positions: 0 Unit cell: (115.7, 167.7, 234, 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 29 16.00 O 3552 8.00 N 3058 7.00 C 11933 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 758.3 milliseconds 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4558 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 38 sheets defined 8.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.794A pdb=" N VAL A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.020A pdb=" N TYR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.509A pdb=" N GLN B 43 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.777A pdb=" N VAL B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 502 through 508 removed outlier: 4.014A pdb=" N ARG C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN C 506 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'E' and resid 66 through 69 Processing helix chain 'E' and resid 113 through 116 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 168 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 33 current: chain 'A' and resid 137 through 147 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 137 through 147 current: chain 'A' and resid 354 through 356 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.804A pdb=" N ASN A 116 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS B 340 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 51 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL B 342 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.748A pdb=" N PHE C 293 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 105 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 103 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 293 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 293 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 227 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 215 through 227 current: chain 'A' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 325 through 335 current: chain 'A' and resid 406 through 410 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 406 through 410 current: chain 'A' and resid 454 through 460 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 239 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 396 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 392 through 396 current: chain 'A' and resid 468 through 474 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 468 through 474 current: chain 'A' and resid 535 through 542 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 535 through 542 current: chain 'A' and resid 577 through 588 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 577 through 588 current: chain 'D' and resid 96 through 101 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 443 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 443 current: chain 'C' and resid 140 through 157 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 157 current: chain 'C' and resid 355 through 356 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 524 through 529 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 33 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 33 current: chain 'B' and resid 137 through 157 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 157 current: chain 'B' and resid 355 through 356 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 215 through 227 current: chain 'B' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 325 through 335 current: chain 'B' and resid 406 through 411 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 406 through 411 current: chain 'B' and resid 454 through 460 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 396 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 396 current: chain 'B' and resid 468 through 474 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 468 through 474 current: chain 'B' and resid 536 through 542 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 536 through 542 current: chain 'B' and resid 578 through 582 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 523 through 529 removed outlier: 3.524A pdb=" N TYR B 558 " --> pdb=" O HIS B 621 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 262 removed outlier: 4.266A pdb=" N ASN C 328 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 320 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU C 216 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 375 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N VAL C 372 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR C 457 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 431 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 406 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN C 383 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 225 through 227 Processing sheet with id=AB7, first strand: chain 'C' and resid 233 through 239 Processing sheet with id=AB8, first strand: chain 'C' and resid 392 through 396 removed outlier: 5.271A pdb=" N ALA C 422 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER C 468 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER C 511 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU C 540 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN C 513 " --> pdb=" O GLU C 540 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR C 542 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE C 515 " --> pdb=" O THR C 542 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE C 603 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN C 563 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY C 564 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 587 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 566 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN C 585 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 568 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 581 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 522 through 525 removed outlier: 4.364A pdb=" N GLY C 522 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS C 524 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 60 removed outlier: 4.701A pdb=" N ASN D 12 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 24 through 28 Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 70 Processing sheet with id=AC5, first strand: chain 'D' and resid 110 through 113 Processing sheet with id=AC6, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC7, first strand: chain 'E' and resid 48 through 51 Processing sheet with id=AC8, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.835A pdb=" N SER F 128 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 139 through 143 Processing sheet with id=AD1, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AD3, first strand: chain 'E' and resid 236 through 237 removed outlier: 3.554A pdb=" N ARG E 247 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 260 through 264 Processing sheet with id=AD5, first strand: chain 'F' and resid 81 through 86 removed outlier: 3.778A pdb=" N GLU F 166 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 47 through 51 Processing sheet with id=AD7, first strand: chain 'F' and resid 94 through 98 Processing sheet with id=AD8, first strand: chain 'F' and resid 139 through 144 Processing sheet with id=AD9, first strand: chain 'F' and resid 175 through 182 Processing sheet with id=AE1, first strand: chain 'F' and resid 188 through 190 Processing sheet with id=AE2, first strand: chain 'F' and resid 236 through 238 437 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5735 1.33 - 1.45: 2914 1.45 - 1.57: 10246 1.57 - 1.69: 1 1.69 - 1.81: 43 Bond restraints: 18939 Sorted by residual: bond pdb=" N PRO C 531 " pdb=" CD PRO C 531 " ideal model delta sigma weight residual 1.473 1.293 0.180 1.40e-02 5.10e+03 1.65e+02 bond pdb=" CA PHE F 240 " pdb=" C PHE F 240 " ideal model delta sigma weight residual 1.524 1.607 -0.083 1.66e-02 3.63e+03 2.49e+01 bond pdb=" CA TYR A 578 " pdb=" C TYR A 578 " ideal model delta sigma weight residual 1.521 1.486 0.034 1.24e-02 6.50e+03 7.71e+00 bond pdb=" N ASN B 66 " pdb=" CA ASN B 66 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.17e-02 7.31e+03 7.61e+00 bond pdb=" N ILE B 70 " pdb=" CA ILE B 70 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.23e-02 6.61e+03 7.40e+00 ... (remaining 18934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 25781 5.65 - 11.30: 35 11.30 - 16.94: 2 16.94 - 22.59: 0 22.59 - 28.24: 1 Bond angle restraints: 25819 Sorted by residual: angle pdb=" N SER F 241 " pdb=" CA SER F 241 " pdb=" C SER F 241 " ideal model delta sigma weight residual 111.03 98.47 12.56 1.11e+00 8.12e-01 1.28e+02 angle pdb=" N LYS C 550 " pdb=" CA LYS C 550 " pdb=" C LYS C 550 " ideal model delta sigma weight residual 111.00 82.76 28.24 2.80e+00 1.28e-01 1.02e+02 angle pdb=" CA PRO C 531 " pdb=" N PRO C 531 " pdb=" CD PRO C 531 " ideal model delta sigma weight residual 112.00 123.80 -11.80 1.40e+00 5.10e-01 7.11e+01 angle pdb=" C PHE F 240 " pdb=" CA PHE F 240 " pdb=" CB PHE F 240 " ideal model delta sigma weight residual 110.81 100.09 10.72 1.73e+00 3.34e-01 3.84e+01 angle pdb=" CA PHE F 240 " pdb=" C PHE F 240 " pdb=" N SER F 241 " ideal model delta sigma weight residual 117.96 110.48 7.48 1.23e+00 6.61e-01 3.70e+01 ... (remaining 25814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 9788 17.78 - 35.57: 1037 35.57 - 53.35: 255 53.35 - 71.13: 47 71.13 - 88.91: 11 Dihedral angle restraints: 11138 sinusoidal: 4044 harmonic: 7094 Sorted by residual: dihedral pdb=" C LYS C 550 " pdb=" N LYS C 550 " pdb=" CA LYS C 550 " pdb=" CB LYS C 550 " ideal model delta harmonic sigma weight residual -122.60 -108.97 -13.63 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" N GLN B 585 " pdb=" C GLN B 585 " pdb=" CA GLN B 585 " pdb=" CB GLN B 585 " ideal model delta harmonic sigma weight residual 122.80 134.13 -11.33 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" C TYR A 578 " pdb=" N TYR A 578 " pdb=" CA TYR A 578 " pdb=" CB TYR A 578 " ideal model delta harmonic sigma weight residual -122.60 -111.53 -11.07 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 11135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2654 0.084 - 0.168: 308 0.168 - 0.252: 20 0.252 - 0.336: 6 0.336 - 0.420: 2 Chirality restraints: 2990 Sorted by residual: chirality pdb=" CA GLN B 585 " pdb=" N GLN B 585 " pdb=" C GLN B 585 " pdb=" CB GLN B 585 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ILE F 239 " pdb=" N ILE F 239 " pdb=" C ILE F 239 " pdb=" CB ILE F 239 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA LYS C 550 " pdb=" N LYS C 550 " pdb=" C LYS C 550 " pdb=" CB LYS C 550 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2987 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 64 " -0.436 9.50e-02 1.11e+02 1.96e-01 2.34e+01 pdb=" NE ARG B 64 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 64 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 64 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 64 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 100 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.04e+00 pdb=" N PRO E 101 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 101 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 101 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 100 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO F 101 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 101 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 101 " -0.026 5.00e-02 4.00e+02 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 11 2.27 - 2.93: 8309 2.93 - 3.58: 24581 3.58 - 4.24: 44517 4.24 - 4.90: 75165 Nonbonded interactions: 152583 Sorted by model distance: nonbonded pdb=" CD2 LEU F 198 " pdb=" O VAL F 248 " model vdw 1.610 3.460 nonbonded pdb=" CG LEU F 198 " pdb=" O VAL F 248 " model vdw 1.791 3.470 nonbonded pdb=" CD1 LEU F 198 " pdb=" O VAL F 248 " model vdw 1.792 3.460 nonbonded pdb=" CE2 PHE C 461 " pdb=" OD1 ASN C 513 " model vdw 1.927 3.340 nonbonded pdb=" CD2 LEU F 198 " pdb=" C VAL F 248 " model vdw 2.045 3.690 ... (remaining 152578 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 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 114 or (resid 115 and (name N or name CA or n \ ame C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB )) or resid 130 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throu \ gh 136 or resid 138 through 172 or (resid 173 and (name N or name CA or name C o \ r name O or name CB )) or resid 174 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 256 or (resid 257 an \ d (name N or name CA or name C or name O or name CB )) or resid 258 through 353 \ or (resid 354 and (name N or name CA or name C or name O or name CB )) or resid \ 355 through 397 or resid 402 through 403 or resid 405 through 448 or (resid 449 \ through 451 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 2 through 463 or resid 465 through 515 or resid 517 or resid 523 through 545 or \ (resid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 \ or (resid 550 through 551 and (name N or name CA or name C or name O or name CB \ )) or resid 552 or (resid 553 through 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 575 or resid 577 through 582 or (resid \ 583 through 586 and (name N or name CA or name C or name O or name CB )) or resi \ d 587 through 595 or (resid 596 through 598 and (name N or name CA or name C or \ name O or name CB )) or resid 599 or (resid 600 and (name N or name CA or name C \ or name O or name CB )) or resid 601 through 622 or (resid 623 through 624 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 23 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 114 or (resid 115 and (name N or n \ ame CA or name C or name O or name CB )) or resid 116 through 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 13 \ 1 or (resid 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 through 134 or (resid 135 and (name N or name CA or name C or name O or na \ me CB )) or resid 136 or resid 138 through 164 or (resid 165 through 166 and (na \ me N or name CA or name C or name O or name CB )) or resid 167 through 172 or (r \ esid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 t \ hrough 177 or (resid 179 and (name N or name CA or name C or name O or name CB ) \ ) or resid 180 through 186 or (resid 187 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 208 and (name N or name CA or name C or name O or na \ me CB )) or resid 209 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 239 or (resid 240 through 241 and \ (name N or name CA or name C or name O or name CB )) or resid 242 through 252 or \ (resid 253 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 4 through 256 or (resid 257 and (name N or name CA or name C or name O or name C \ B )) or resid 258 through 266 or (resid 267 and (name N or name CA or name C or \ name O or name CB )) or resid 268 through 270 or (resid 271 and (name N or name \ CA or name C or name O or name CB )) or resid 272 through 274 or (resid 275 and \ (name N or name CA or name C or name O or name CB )) or resid 276 through 277 or \ (resid 278 through 280 and (name N or name CA or name C or name O or name CB )) \ or resid 281 through 283 or (resid 284 and (name N or name CA or name C or name \ O or name CB )) or resid 285 through 297 or (resid 298 through 299 and (name N \ or name CA or name C or name O or name CB )) or resid 300 through 302 or (resid \ 303 and (name N or name CA or name C or name O or name CB )) or resid 304 throug \ h 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or \ resid 318 through 347 or resid 352 through 353 or (resid 354 and (name N or name \ CA or name C or name O or name CB )) or resid 355 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 360 through 367 o \ r (resid 368 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 69 through 397 or (resid 402 through 403 and (name N or name CA or name C or nam \ e O or name CB )) or resid 405 through 413 or (resid 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 422 or (resid 423 through \ 424 and (name N or name CA or name C or name O or name CB )) or resid 425 throu \ gh 432 or (resid 433 through 434 and (name N or name CA or name C or name O or n \ ame CB )) or resid 435 through 445 or (resid 446 and (name N or name CA or name \ C or name O or name CB )) or resid 447 through 448 or (resid 449 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 462 o \ r (resid 463 through 466 and (name N or name CA or name C or name O or name CB ) \ ) or resid 467 through 475 or (resid 476 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 478 and (name N or name CA or name C or name O or na \ me CB )) or resid 479 through 485 or (resid 486 and (name N or name CA or name C \ or name O or name CB )) or resid 493 through 495 or (resid 496 and (name N or n \ ame CA or name C or name O or name CB )) or resid 497 through 499 or (resid 500 \ through 501 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 2 through 504 or (resid 505 and (name N or name CA or name C or name O or name C \ B )) or resid 506 through 515 or (resid 517 and (name N or name CA or name C or \ name O or name CB )) or resid 523 through 545 or (resid 546 and (name N or name \ CA or name C or name O or name CB )) or resid 547 or (resid 550 through 551 and \ (name N or name CA or name C or name O or name CB )) or resid 552 or (resid 553 \ through 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 through 572 or (resid 573 and (name N or name CA or name C or name O or name C \ B )) or resid 574 through 575 or resid 577 through 585 or (resid 586 and (name N \ or name CA or name C or name O or name CB )) or resid 587 or (resid 588 and (na \ me N or name CA or name C or name O or name CB )) or resid 589 through 592 or (r \ esid 593 through 594 and (name N or name CA or name C or name O or name CB )) or \ resid 595 through 599 or (resid 600 and (name N or name CA or name C or name O \ or name CB )) or resid 601 through 612 or (resid 613 and (name N or name CA or n \ ame C or name O or name CB )) or resid 614 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 622 or (resid \ 623 through 624 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 66 or (resid 67 and (name N or name CA or nam \ e C or name O or name CB )) or resid 68 through 165 or (resid 166 and (name N or \ name CA or name C or name O or name CB )) or resid 167 through 177 or (resid 17 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 180 through \ 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or re \ sid 208 through 239 or (resid 240 through 241 and (name N or name CA or name C o \ r name O or name CB )) or resid 242 through 252 or (resid 253 and (name N or nam \ e CA or name C or name O or name CB )) or resid 254 through 270 or (resid 271 an \ d (name N or name CA or name C or name O or name CB )) or resid 272 through 274 \ or (resid 275 and (name N or name CA or name C or name O or name CB )) or resid \ 276 through 277 or (resid 278 through 280 and (name N or name CA or name C or na \ me O or name CB )) or resid 281 through 347 or resid 352 through 358 or (resid 3 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or r \ esid 369 through 397 or (resid 403 through 404 and (name N or name CA or name C \ or name O or name CB )) or resid 405 through 413 or (resid 414 and (name N or na \ me CA or name C or name O or name CB )) or resid 415 through 422 or (resid 423 t \ hrough 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 432 or (resid 433 through 434 and (name N or name CA or name C or name \ O or name CB )) or resid 435 through 445 or (resid 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 through 462 or (resid 463 through 4 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 467 through \ 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) or ( \ resid 478 and (name N or name CA or name C or name O or name CB )) or resid 479 \ through 485 or (resid 486 and (name N or name CA or name C or name O or name CB \ )) or resid 493 through 495 or (resid 496 and (name N or name CA or name C or na \ me O or name CB )) or resid 497 through 499 or (resid 500 through 501 and (name \ N or name CA or name C or name O or name CB )) or resid 502 through 515 or resid \ 519 or resid 523 through 553 or (resid 554 through 556 and (name N or name CA o \ r name C or name O or name CB )) or resid 557 through 582 or (resid 583 through \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 or (re \ sid 588 and (name N or name CA or name C or name O or name CB )) or resid 589 th \ rough 592 or (resid 593 through 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 or (resid 596 through 598 and (name N or name CA or na \ me C or name O or name CB )) or resid 599 through 612 or (resid 613 and (name N \ or name CA or name C or name O or name CB )) or resid 614 through 618 or (resid \ 619 and (name N or name CA or name C or name O or name CB )) or resid 620 throug \ h 624)) } ncs_group { reference = (chain 'E' and (resid 32 or (resid 33 through 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 41 or (resid 42 through 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 and ( \ name N or name CA or name C or name O or name CB )) or resid 47 through 78 or (r \ esid 79 through 81 and (name N or name CA or name C or name O or name CB )) or r \ esid 82 through 91 or (resid 92 through 93 and (name N or name CA or name C or n \ ame O or name CB )) or resid 94 through 143 or (resid 144 and (name N or name CA \ or name C or name O or name CB )) or resid 145 or (resid 146 through 147 and (n \ ame N or name CA or name C or name O or name CB )) or resid 148 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 195 \ through 203 or (resid 204 and (name N or name CA or name C or name O or name CB \ )) or resid 205 through 207 or (resid 208 and (name N or name CA or name C or na \ me O or name CB )) or resid 209 through 217 or resid 219 through 224 or (resid 2 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 226 through \ 229 or (resid 230 through 235 and (name N or name CA or name C or name O or nam \ e CB )) or resid 236 through 238 or (resid 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 through 248 or (resid 249 through 258 and ( \ name N or name CA or name C or name O or name CB )) or resid 259 through 260 or \ (resid 261 and (name N or name CA or name C or name O or name CB )) or resid 262 \ through 280 or resid 283 through 289 or (resid 292 through 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 304 or (resid 307 \ through 308 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 9 through 315)) selection = (chain 'F' and (resid 32 through 90 or (resid 91 through 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 108 or (resid 109 throu \ gh 110 and (name N or name CA or name C or name O or name CB )) or resid 111 thr \ ough 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) \ or resid 115 through 126 or (resid 127 and (name N or name CA or name C or name \ O or name CB )) or resid 128 through 150 or (resid 151 and (name N or name CA or \ name C or name O or name CB )) or resid 152 through 177 or resid 179 through 18 \ 3 or resid 186 through 191 or (resid 195 and (name N or name CA or name C or nam \ e O or name CB )) or resid 196 through 210 or (resid 211 through 212 and (name N \ or name CA or name C or name O or name CB )) or resid 213 through 230 or (resid \ 231 through 232 and (name N or name CA or name C or name O or name CB )) or (re \ sid 235 and (name N or name CA or name C or name O or name CB )) or resid 236 th \ rough 237 or (resid 238 through 239 and (name N or name CA or name C or name O o \ r name CB )) or resid 240 or (resid 242 through 244 and (name N or name CA or na \ me C or name O or name CB )) or resid 245 through 249 or (resid 253 through 258 \ and (name N or name CA or name C or name O or name CB )) or resid 259 through 26 \ 9 or (resid 270 and (name N or name CA or name C or name O or name CB )) or resi \ d 271 through 285 or (resid 286 through 287 and (name N or name CA or name C or \ name O or name CB )) or (resid 288 through 293 and (name N or name CA or name C \ or name O or name CB )) or resid 294 through 300 or (resid 301 through 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 312 or \ (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ or (resid 315 and (name N or name CA or name C or name O or name CB or name OXT \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.330 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.276 18940 Z= 0.308 Angle : 0.723 28.239 25819 Z= 0.415 Chirality : 0.053 0.420 2990 Planarity : 0.005 0.196 3315 Dihedral : 15.719 88.914 6580 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.17 % Favored : 93.57 % Rotamer: Outliers : 1.29 % Allowed : 22.51 % Favored : 76.20 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.20 % 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: -1.25 (0.17), residues: 2333 helix: -0.08 (0.49), residues: 118 sheet: -0.19 (0.16), residues: 987 loop : -1.44 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 54 TYR 0.014 0.001 TYR C 525 PHE 0.015 0.002 PHE C 442 TRP 0.023 0.002 TRP F 205 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00476 (18939) covalent geometry : angle 0.72269 (25819) hydrogen bonds : bond 0.14038 ( 437) hydrogen bonds : angle 7.58390 ( 1092) Misc. bond : bond 0.27566 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 261 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7868 (p) REVERT: A 418 TYR cc_start: 0.7906 (m-80) cc_final: 0.7613 (m-80) REVERT: A 499 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7152 (ttt180) REVERT: E 201 ASN cc_start: 0.7409 (m110) cc_final: 0.7123 (m-40) REVERT: F 51 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: F 76 ASP cc_start: 0.7375 (t0) cc_final: 0.7051 (t70) REVERT: F 114 ASP cc_start: 0.8415 (m-30) cc_final: 0.7851 (t0) REVERT: F 238 TRP cc_start: 0.6784 (t60) cc_final: 0.6361 (t60) outliers start: 25 outliers final: 14 residues processed: 115 average time/residue: 0.4407 time to fit residues: 60.5753 Evaluate side-chains 105 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 439 ASN B 178 ASN B 529 GLN C 178 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079959 restraints weight = 39556.370| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.83 r_work: 0.3175 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18940 Z= 0.194 Angle : 0.553 8.442 25819 Z= 0.297 Chirality : 0.046 0.158 2990 Planarity : 0.003 0.071 3315 Dihedral : 5.862 59.905 2627 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer: Outliers : 2.89 % Allowed : 21.58 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.14 (0.17), residues: 2333 helix: 1.10 (0.53), residues: 96 sheet: -0.24 (0.16), residues: 1008 loop : -1.35 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 54 TYR 0.019 0.001 TYR B 120 PHE 0.020 0.002 PHE C 293 TRP 0.016 0.001 TRP F 205 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00457 (18939) covalent geometry : angle 0.55320 (25819) hydrogen bonds : bond 0.03885 ( 437) hydrogen bonds : angle 6.47031 ( 1092) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.775 Fit side-chains REVERT: A 23 ILE cc_start: 0.9122 (tp) cc_final: 0.8804 (tt) REVERT: A 391 ASP cc_start: 0.8641 (m-30) cc_final: 0.8323 (t70) REVERT: A 499 ARG cc_start: 0.8156 (ttt-90) cc_final: 0.7309 (ttt180) REVERT: B 120 TYR cc_start: 0.6759 (t80) cc_final: 0.6544 (t80) REVERT: B 122 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8492 (pt0) REVERT: B 456 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (m-40) REVERT: B 524 HIS cc_start: 0.8173 (m90) cc_final: 0.7971 (m90) REVERT: C 442 PHE cc_start: 0.8403 (t80) cc_final: 0.8165 (t80) REVERT: E 201 ASN cc_start: 0.7363 (m110) cc_final: 0.7084 (m-40) REVERT: E 209 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7864 (mm) REVERT: F 76 ASP cc_start: 0.7419 (t0) cc_final: 0.7007 (t70) REVERT: F 114 ASP cc_start: 0.8269 (m-30) cc_final: 0.7794 (t0) REVERT: F 174 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7943 (ptpt) REVERT: F 238 TRP cc_start: 0.7007 (t60) cc_final: 0.6563 (t60) outliers start: 56 outliers final: 17 residues processed: 149 average time/residue: 0.3906 time to fit residues: 70.7021 Evaluate side-chains 109 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 230 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 178 ASN C 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080189 restraints weight = 39842.542| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.84 r_work: 0.3179 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18940 Z= 0.175 Angle : 0.540 9.364 25819 Z= 0.288 Chirality : 0.046 0.163 2990 Planarity : 0.003 0.066 3315 Dihedral : 5.275 58.940 2611 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.13 % Favored : 93.70 % Rotamer: Outliers : 2.94 % Allowed : 21.48 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.09 (0.17), residues: 2333 helix: 1.28 (0.53), residues: 90 sheet: -0.19 (0.16), residues: 1008 loop : -1.33 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.023 0.001 TYR B 120 PHE 0.018 0.001 PHE C 293 TRP 0.013 0.001 TRP C 38 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00413 (18939) covalent geometry : angle 0.53970 (25819) hydrogen bonds : bond 0.03661 ( 437) hydrogen bonds : angle 6.24541 ( 1092) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 97 time to evaluate : 0.700 Fit side-chains REVERT: A 23 ILE cc_start: 0.9058 (tp) cc_final: 0.8752 (tt) REVERT: A 63 LEU cc_start: 0.9004 (tt) cc_final: 0.8766 (tm) REVERT: A 391 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8338 (t70) REVERT: A 499 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7439 (ttt180) REVERT: A 597 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: B 456 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: B 524 HIS cc_start: 0.8175 (m90) cc_final: 0.7963 (m90) REVERT: C 442 PHE cc_start: 0.8454 (t80) cc_final: 0.8235 (t80) REVERT: E 201 ASN cc_start: 0.7269 (m110) cc_final: 0.7004 (m-40) REVERT: E 209 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7959 (mm) REVERT: F 76 ASP cc_start: 0.7436 (t0) cc_final: 0.7017 (t70) REVERT: F 114 ASP cc_start: 0.8276 (m-30) cc_final: 0.7792 (t0) REVERT: F 174 LYS cc_start: 0.8262 (ptmm) cc_final: 0.7995 (ptpt) REVERT: F 238 TRP cc_start: 0.7006 (t60) cc_final: 0.6469 (t60) outliers start: 57 outliers final: 22 residues processed: 146 average time/residue: 0.2987 time to fit residues: 54.0455 Evaluate side-chains 117 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 237 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 130 optimal weight: 0.1980 chunk 168 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 148 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081684 restraints weight = 39461.655| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.84 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18940 Z= 0.122 Angle : 0.504 9.545 25819 Z= 0.269 Chirality : 0.046 0.167 2990 Planarity : 0.003 0.065 3315 Dihedral : 4.915 57.980 2604 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 2.94 % Allowed : 21.63 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.17), residues: 2333 helix: 1.36 (0.53), residues: 90 sheet: -0.10 (0.16), residues: 1015 loop : -1.29 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.014 0.001 TYR F 272 PHE 0.015 0.001 PHE C 293 TRP 0.014 0.001 TRP F 205 HIS 0.002 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00284 (18939) covalent geometry : angle 0.50366 (25819) hydrogen bonds : bond 0.03269 ( 437) hydrogen bonds : angle 6.00452 ( 1092) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 98 time to evaluate : 0.519 Fit side-chains REVERT: A 23 ILE cc_start: 0.9074 (tp) cc_final: 0.8777 (tt) REVERT: A 391 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8411 (t70) REVERT: A 473 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 499 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7324 (ttt180) REVERT: A 570 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7167 (ttt180) REVERT: A 597 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8201 (mmm-85) REVERT: A 624 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6919 (pp) REVERT: B 524 HIS cc_start: 0.8128 (m90) cc_final: 0.7881 (m90) REVERT: C 290 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8357 (t) REVERT: E 201 ASN cc_start: 0.7312 (m110) cc_final: 0.7043 (m-40) REVERT: E 277 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8839 (tt) REVERT: E 310 TRP cc_start: 0.8038 (m100) cc_final: 0.7133 (m100) REVERT: F 76 ASP cc_start: 0.7377 (t0) cc_final: 0.6982 (t70) REVERT: F 114 ASP cc_start: 0.8245 (m-30) cc_final: 0.7763 (t0) REVERT: F 174 LYS cc_start: 0.8273 (ptmm) cc_final: 0.8010 (ptpt) REVERT: F 238 TRP cc_start: 0.6876 (t60) cc_final: 0.6402 (t60) outliers start: 57 outliers final: 22 residues processed: 148 average time/residue: 0.2993 time to fit residues: 54.9325 Evaluate side-chains 121 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081716 restraints weight = 39373.021| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.84 r_work: 0.3204 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18940 Z= 0.128 Angle : 0.508 12.445 25819 Z= 0.269 Chirality : 0.046 0.225 2990 Planarity : 0.003 0.062 3315 Dihedral : 4.835 57.744 2603 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 3.20 % Allowed : 21.37 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.92 (0.17), residues: 2333 helix: 1.39 (0.53), residues: 90 sheet: -0.07 (0.16), residues: 1025 loop : -1.24 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.014 0.001 TYR C 310 PHE 0.015 0.001 PHE C 293 TRP 0.011 0.001 TRP C 38 HIS 0.002 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00300 (18939) covalent geometry : angle 0.50758 (25819) hydrogen bonds : bond 0.03250 ( 437) hydrogen bonds : angle 5.91632 ( 1092) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 100 time to evaluate : 0.638 Fit side-chains REVERT: A 23 ILE cc_start: 0.9079 (tp) cc_final: 0.8780 (tt) REVERT: A 391 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8468 (t70) REVERT: A 473 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 499 ARG cc_start: 0.8408 (ttt-90) cc_final: 0.7642 (ttt180) REVERT: A 515 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 597 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: A 624 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7012 (pp) REVERT: B 120 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 524 HIS cc_start: 0.8130 (m90) cc_final: 0.7880 (m90) REVERT: B 599 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7092 (pp) REVERT: C 290 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 329 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8449 (mtpm) REVERT: C 424 ASN cc_start: 0.8659 (m110) cc_final: 0.8394 (OUTLIER) REVERT: D 54 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8742 (ttm-80) REVERT: E 166 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: E 201 ASN cc_start: 0.7552 (m110) cc_final: 0.7303 (m-40) REVERT: E 277 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8856 (tt) REVERT: E 310 TRP cc_start: 0.7910 (m100) cc_final: 0.7703 (m100) REVERT: F 76 ASP cc_start: 0.7445 (t0) cc_final: 0.7057 (t70) REVERT: F 114 ASP cc_start: 0.8340 (m-30) cc_final: 0.7833 (t0) REVERT: F 174 LYS cc_start: 0.8247 (ptmm) cc_final: 0.8002 (ptpt) REVERT: F 238 TRP cc_start: 0.6874 (t60) cc_final: 0.6343 (t60) outliers start: 62 outliers final: 28 residues processed: 157 average time/residue: 0.3556 time to fit residues: 68.0846 Evaluate side-chains 131 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 209 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 66 ASN E 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079864 restraints weight = 39462.997| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.84 r_work: 0.3172 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18940 Z= 0.194 Angle : 0.548 11.060 25819 Z= 0.291 Chirality : 0.047 0.203 2990 Planarity : 0.003 0.060 3315 Dihedral : 5.045 59.066 2603 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.31 % Rotamer: Outliers : 3.15 % Allowed : 21.68 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.97 (0.17), residues: 2333 helix: 1.43 (0.53), residues: 90 sheet: -0.13 (0.16), residues: 1022 loop : -1.25 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.015 0.002 TYR A 120 PHE 0.020 0.002 PHE C 293 TRP 0.019 0.001 TRP F 205 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00460 (18939) covalent geometry : angle 0.54780 (25819) hydrogen bonds : bond 0.03586 ( 437) hydrogen bonds : angle 6.07449 ( 1092) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 93 time to evaluate : 0.701 Fit side-chains REVERT: A 23 ILE cc_start: 0.9073 (tp) cc_final: 0.8762 (tt) REVERT: A 391 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8384 (t70) REVERT: A 473 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 499 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.7888 (ttm-80) REVERT: A 597 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: B 70 ILE cc_start: 0.8887 (pt) cc_final: 0.8600 (pp) REVERT: B 477 ASP cc_start: 0.8166 (p0) cc_final: 0.7360 (t0) REVERT: B 599 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7053 (pp) REVERT: C 329 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8452 (mtpm) REVERT: C 424 ASN cc_start: 0.8714 (m110) cc_final: 0.8431 (OUTLIER) REVERT: D 54 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8737 (ttm-80) REVERT: E 70 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: E 166 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: E 201 ASN cc_start: 0.7240 (m110) cc_final: 0.7008 (m-40) REVERT: E 277 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8840 (tt) REVERT: F 76 ASP cc_start: 0.7558 (t0) cc_final: 0.7144 (t70) REVERT: F 114 ASP cc_start: 0.8491 (m-30) cc_final: 0.8048 (t0) REVERT: F 174 LYS cc_start: 0.8251 (ptmm) cc_final: 0.8017 (ptpt) REVERT: F 238 TRP cc_start: 0.6890 (t60) cc_final: 0.6269 (t60) REVERT: F 274 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7720 (mt) outliers start: 61 outliers final: 29 residues processed: 146 average time/residue: 0.3546 time to fit residues: 63.6838 Evaluate side-chains 124 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 98 optimal weight: 0.0010 chunk 226 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 212 optimal weight: 0.6980 chunk 202 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082268 restraints weight = 39649.582| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.85 r_work: 0.3216 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18940 Z= 0.111 Angle : 0.499 10.246 25819 Z= 0.264 Chirality : 0.045 0.210 2990 Planarity : 0.003 0.060 3315 Dihedral : 4.784 58.021 2603 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 2.84 % Allowed : 21.84 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.17), residues: 2333 helix: 1.30 (0.53), residues: 92 sheet: -0.04 (0.16), residues: 1025 loop : -1.15 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.013 0.001 TYR C 310 PHE 0.015 0.001 PHE C 293 TRP 0.022 0.001 TRP F 205 HIS 0.002 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00254 (18939) covalent geometry : angle 0.49945 (25819) hydrogen bonds : bond 0.03065 ( 437) hydrogen bonds : angle 5.84306 ( 1092) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 0.752 Fit side-chains REVERT: A 23 ILE cc_start: 0.9117 (tp) cc_final: 0.8770 (tt) REVERT: A 391 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8482 (t70) REVERT: A 499 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.7940 (ttm-80) REVERT: A 597 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: A 624 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7021 (pp) REVERT: B 120 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7063 (t80) REVERT: B 599 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7044 (pp) REVERT: C 329 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (mtpm) REVERT: C 530 SER cc_start: 0.8775 (t) cc_final: 0.8332 (m) REVERT: D 54 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8744 (ttm-80) REVERT: E 70 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: E 166 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: E 201 ASN cc_start: 0.7348 (m110) cc_final: 0.7137 (m-40) REVERT: E 277 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (tt) REVERT: F 51 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: F 76 ASP cc_start: 0.7433 (t0) cc_final: 0.7061 (t70) REVERT: F 114 ASP cc_start: 0.8324 (m-30) cc_final: 0.7832 (t0) REVERT: F 174 LYS cc_start: 0.8217 (ptmm) cc_final: 0.8009 (ptpt) REVERT: F 238 TRP cc_start: 0.6345 (t60) cc_final: 0.5886 (t60) REVERT: F 274 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7762 (mt) outliers start: 55 outliers final: 26 residues processed: 146 average time/residue: 0.3606 time to fit residues: 63.9542 Evaluate side-chains 128 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 220 optimal weight: 0.0980 chunk 219 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081902 restraints weight = 39345.355| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.85 r_work: 0.3210 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18940 Z= 0.126 Angle : 0.510 10.525 25819 Z= 0.268 Chirality : 0.046 0.200 2990 Planarity : 0.003 0.058 3315 Dihedral : 4.719 58.326 2601 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.87 % Rotamer: Outliers : 2.53 % Allowed : 22.61 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.82 (0.17), residues: 2333 helix: 1.41 (0.53), residues: 90 sheet: -0.03 (0.16), residues: 1037 loop : -1.14 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.015 0.001 TYR F 272 PHE 0.016 0.001 PHE C 442 TRP 0.015 0.001 TRP F 205 HIS 0.002 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00293 (18939) covalent geometry : angle 0.50966 (25819) hydrogen bonds : bond 0.03149 ( 437) hydrogen bonds : angle 5.83422 ( 1092) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.731 Fit side-chains REVERT: A 23 ILE cc_start: 0.8950 (tp) cc_final: 0.8607 (tt) REVERT: A 391 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8499 (t70) REVERT: A 499 ARG cc_start: 0.8454 (ttt-90) cc_final: 0.7941 (ttm-80) REVERT: A 597 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: A 624 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.7016 (pp) REVERT: B 70 ILE cc_start: 0.8852 (pt) cc_final: 0.8616 (pp) REVERT: B 120 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 586 ASN cc_start: 0.8608 (t0) cc_final: 0.8236 (m-40) REVERT: B 599 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7017 (pp) REVERT: C 329 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8474 (mtpm) REVERT: D 54 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8744 (ttm-80) REVERT: E 70 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7852 (mtp180) REVERT: E 166 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: E 201 ASN cc_start: 0.7358 (m110) cc_final: 0.7136 (m-40) REVERT: E 277 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8832 (tt) REVERT: F 76 ASP cc_start: 0.7452 (t0) cc_final: 0.7073 (t70) REVERT: F 114 ASP cc_start: 0.8428 (m-30) cc_final: 0.7992 (t0) REVERT: F 174 LYS cc_start: 0.8223 (ptmm) cc_final: 0.7998 (ptpt) REVERT: F 238 TRP cc_start: 0.6448 (t60) cc_final: 0.6045 (t60) REVERT: F 274 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (mt) outliers start: 49 outliers final: 27 residues processed: 140 average time/residue: 0.3341 time to fit residues: 57.6381 Evaluate side-chains 126 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 60 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 187 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 213 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080336 restraints weight = 39452.335| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.84 r_work: 0.3179 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18940 Z= 0.182 Angle : 0.549 10.876 25819 Z= 0.289 Chirality : 0.046 0.186 2990 Planarity : 0.003 0.057 3315 Dihedral : 4.931 59.656 2601 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 2.58 % Allowed : 22.56 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.88 (0.17), residues: 2333 helix: 1.46 (0.54), residues: 90 sheet: -0.04 (0.16), residues: 1021 loop : -1.21 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.016 0.001 TYR B 525 PHE 0.018 0.001 PHE C 293 TRP 0.015 0.001 TRP F 205 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00431 (18939) covalent geometry : angle 0.54935 (25819) hydrogen bonds : bond 0.03446 ( 437) hydrogen bonds : angle 6.01150 ( 1092) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 89 time to evaluate : 0.770 Fit side-chains REVERT: A 23 ILE cc_start: 0.9078 (tp) cc_final: 0.8769 (tt) REVERT: A 391 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8504 (t70) REVERT: A 499 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.7960 (ttm-80) REVERT: A 597 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: A 624 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.7037 (pp) REVERT: B 70 ILE cc_start: 0.8846 (pt) cc_final: 0.8609 (pp) REVERT: B 127 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8107 (ttt180) REVERT: B 456 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8526 (m-40) REVERT: B 505 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8228 (mtm110) REVERT: B 599 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7032 (pp) REVERT: C 63 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9198 (tt) REVERT: C 329 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8460 (mtpm) REVERT: D 54 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8751 (ttm-80) REVERT: E 70 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6250 (mtp180) REVERT: E 166 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: E 201 ASN cc_start: 0.7370 (m110) cc_final: 0.7162 (m-40) REVERT: E 277 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8797 (tt) REVERT: F 76 ASP cc_start: 0.7537 (t0) cc_final: 0.7122 (t70) REVERT: F 114 ASP cc_start: 0.8522 (m-30) cc_final: 0.8128 (t0) REVERT: F 174 LYS cc_start: 0.8201 (ptmm) cc_final: 0.7986 (ptpt) REVERT: F 274 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7845 (mt) outliers start: 50 outliers final: 28 residues processed: 132 average time/residue: 0.3699 time to fit residues: 59.2314 Evaluate side-chains 128 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 221 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081680 restraints weight = 39434.625| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.84 r_work: 0.3203 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18940 Z= 0.132 Angle : 0.528 10.768 25819 Z= 0.275 Chirality : 0.046 0.206 2990 Planarity : 0.003 0.054 3315 Dihedral : 4.823 58.914 2601 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.87 % Rotamer: Outliers : 2.32 % Allowed : 22.61 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.80 (0.17), residues: 2333 helix: 1.44 (0.53), residues: 90 sheet: 0.02 (0.16), residues: 1014 loop : -1.15 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.016 0.001 TYR B 525 PHE 0.016 0.001 PHE C 442 TRP 0.027 0.001 TRP F 205 HIS 0.002 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00309 (18939) covalent geometry : angle 0.52807 (25819) hydrogen bonds : bond 0.03174 ( 437) hydrogen bonds : angle 5.90855 ( 1092) Misc. bond : bond 0.00048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.477 Fit side-chains REVERT: A 23 ILE cc_start: 0.8951 (tp) cc_final: 0.8603 (tt) REVERT: A 391 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8510 (t70) REVERT: A 499 ARG cc_start: 0.8450 (ttt-90) cc_final: 0.7949 (ttm-80) REVERT: A 597 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8221 (mmm-85) REVERT: A 624 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.7019 (pp) REVERT: B 70 ILE cc_start: 0.8839 (pt) cc_final: 0.8629 (pp) REVERT: B 120 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 127 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: B 477 ASP cc_start: 0.8144 (p0) cc_final: 0.7286 (t0) REVERT: B 599 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6997 (pp) REVERT: C 329 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8461 (mtpm) REVERT: C 496 LYS cc_start: 0.7560 (mtmm) cc_final: 0.7071 (mttt) REVERT: D 54 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8778 (ttm-80) REVERT: E 70 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6265 (mtp180) REVERT: E 166 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: E 201 ASN cc_start: 0.7352 (m110) cc_final: 0.7148 (m-40) REVERT: E 277 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8797 (tt) REVERT: E 310 TRP cc_start: 0.7749 (m100) cc_final: 0.6353 (m100) REVERT: F 76 ASP cc_start: 0.7460 (t0) cc_final: 0.7080 (t70) REVERT: F 114 ASP cc_start: 0.8489 (m-30) cc_final: 0.8094 (t0) REVERT: F 174 LYS cc_start: 0.8248 (ptmm) cc_final: 0.8026 (ptpt) REVERT: F 274 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (mt) outliers start: 45 outliers final: 29 residues processed: 137 average time/residue: 0.4023 time to fit residues: 65.3392 Evaluate side-chains 132 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 42 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN F 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.101588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079811 restraints weight = 39774.529| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.84 r_work: 0.3170 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18940 Z= 0.207 Angle : 0.569 11.090 25819 Z= 0.298 Chirality : 0.047 0.205 2990 Planarity : 0.003 0.053 3315 Dihedral : 5.033 59.876 2601 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 2.17 % Allowed : 22.77 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.90 (0.17), residues: 2333 helix: 1.42 (0.54), residues: 90 sheet: -0.07 (0.16), residues: 1021 loop : -1.21 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.016 0.002 TYR B 525 PHE 0.020 0.002 PHE C 293 TRP 0.028 0.002 TRP F 205 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00491 (18939) covalent geometry : angle 0.56949 (25819) hydrogen bonds : bond 0.03579 ( 437) hydrogen bonds : angle 6.09045 ( 1092) Misc. bond : bond 0.00090 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.10 seconds wall clock time: 90 minutes 4.51 seconds (5404.51 seconds total)