Starting phenix.real_space_refine on Wed Sep 17 16:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.map" model { file = "/net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j60_33735/09_2025/8j60_33735.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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 38 5.16 5 C 6264 2.51 5 N 1619 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9757 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3659 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 469} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 7, 'GLU:plan': 9, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 218 Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1179 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1167 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 142} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3752 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 484} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 4, 'ASP:plan': 11, 'GLN:plan1': 8, 'GLU:plan': 7, 'ARG:plan': 7, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 221 Time building chain proxies: 2.40, per 1000 atoms: 0.25 Number of scatterers: 9757 At special positions: 0 Unit cell: (154.16, 82.82, 81.18, 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 38 16.00 O 1836 8.00 N 1619 7.00 C 6264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 320 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 301.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 37.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 171 through 176 removed outlier: 4.147A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.714A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 331 through 349 removed outlier: 3.721A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.761A pdb=" N GLU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 434 removed outlier: 3.816A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.323A pdb=" N GLU B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.058A pdb=" N GLU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.607A pdb=" N LYS B 518 " --> pdb=" O LYS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 4.115A pdb=" N ILE B 570 " --> pdb=" O PRO B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.535A pdb=" N LYS B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.623A pdb=" N SER C 13 " --> pdb=" O TRP C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 32 through 54 Processing helix chain 'C' and resid 57 through 75 Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.901A pdb=" N VAL C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 158 Processing helix chain 'D' and resid 13 through 24 removed outlier: 3.548A pdb=" N VAL D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 removed outlier: 3.781A pdb=" N TYR D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 122 through 135 removed outlier: 3.902A pdb=" N VAL D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 158 Processing helix chain 'A' and resid 225 through 241 removed outlier: 3.542A pdb=" N ILE A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.663A pdb=" N ASP A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.633A pdb=" N ASP A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.850A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.661A pdb=" N PHE A 448 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.191A pdb=" N LEU A 497 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 3.805A pdb=" N LYS A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.853A pdb=" N ILE A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 4.033A pdb=" N ARG A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.584A pdb=" N ILE B 78 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 158 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 161 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 97 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 163 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 95 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 91 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.584A pdb=" N ILE B 78 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 158 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 161 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 97 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 163 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 95 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 319 removed outlier: 5.134A pdb=" N SER B 317 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS B 300 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN B 319 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 298 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 435 through 437 removed outlier: 3.852A pdb=" N ASP B 437 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 455 removed outlier: 7.380A pdb=" N ILE B 538 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 532 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN B 540 " --> pdb=" O HIS B 530 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE B 523 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS B 491 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 525 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 464 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ARG B 560 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 466 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 586 through 587 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 81 Processing sheet with id=AB2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.737A pdb=" N LYS A 90 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.654A pdb=" N ILE A 126 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AB6, first strand: chain 'A' and resid 319 through 321 removed outlier: 4.008A pdb=" N GLN A 319 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 298 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 465 through 467 removed outlier: 6.487A pdb=" N THR A 466 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 489 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG A 525 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 491 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A 523 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 530 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 540 " --> pdb=" O HIS A 530 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1140 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: 1.36 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3145 1.35 - 1.47: 2488 1.47 - 1.60: 4266 1.60 - 1.73: 0 1.73 - 1.85: 64 Bond restraints: 9963 Sorted by residual: bond pdb=" CB PRO A 445 " pdb=" CG PRO A 445 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.23e+00 bond pdb=" C TYR B 211 " pdb=" O TYR B 211 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.26e+00 bond pdb=" CA CYS A 320 " pdb=" CB CYS A 320 " ideal model delta sigma weight residual 1.527 1.552 -0.026 1.75e-02 3.27e+03 2.13e+00 bond pdb=" CG LEU D 66 " pdb=" CD2 LEU D 66 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" CB CYS A 320 " pdb=" SG CYS A 320 " ideal model delta sigma weight residual 1.808 1.851 -0.043 3.30e-02 9.18e+02 1.70e+00 ... (remaining 9958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13300 2.38 - 4.76: 224 4.76 - 7.14: 28 7.14 - 9.52: 12 9.52 - 11.90: 3 Bond angle restraints: 13567 Sorted by residual: angle pdb=" N PRO A 121 " pdb=" CA PRO A 121 " pdb=" CB PRO A 121 " ideal model delta sigma weight residual 103.25 111.34 -8.09 1.05e+00 9.07e-01 5.93e+01 angle pdb=" N PRO B 400 " pdb=" CA PRO B 400 " pdb=" CB PRO B 400 " ideal model delta sigma weight residual 102.60 110.28 -7.68 1.10e+00 8.26e-01 4.88e+01 angle pdb=" N PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 102.33 110.17 -7.84 1.18e+00 7.18e-01 4.41e+01 angle pdb=" N PRO D 102 " pdb=" CA PRO D 102 " pdb=" CB PRO D 102 " ideal model delta sigma weight residual 103.25 110.21 -6.96 1.05e+00 9.07e-01 4.40e+01 angle pdb=" N ILE B 365 " pdb=" CA ILE B 365 " pdb=" C ILE B 365 " ideal model delta sigma weight residual 113.53 107.24 6.29 9.80e-01 1.04e+00 4.12e+01 ... (remaining 13562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5318 17.19 - 34.37: 476 34.37 - 51.56: 93 51.56 - 68.75: 10 68.75 - 85.93: 12 Dihedral angle restraints: 5909 sinusoidal: 2108 harmonic: 3801 Sorted by residual: dihedral pdb=" CA CYS B 295 " pdb=" C CYS B 295 " pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA GLN B 319 " pdb=" C GLN B 319 " pdb=" N CYS B 320 " pdb=" CA CYS B 320 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS A 295 " pdb=" C CYS A 295 " pdb=" N ILE A 296 " pdb=" CA ILE A 296 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1265 0.051 - 0.101: 276 0.101 - 0.152: 60 0.152 - 0.203: 5 0.203 - 0.253: 4 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CA PRO D 102 " pdb=" N PRO D 102 " pdb=" C PRO D 102 " pdb=" CB PRO D 102 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO B 400 " pdb=" N PRO B 400 " pdb=" C PRO B 400 " pdb=" CB PRO B 400 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1607 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 450 " 0.095 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO A 451 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 444 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 445 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 449 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO B 450 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 450 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 450 " 0.037 5.00e-02 4.00e+02 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 144 2.66 - 3.22: 9621 3.22 - 3.78: 14818 3.78 - 4.34: 19794 4.34 - 4.90: 32990 Nonbonded interactions: 77367 Sorted by model distance: nonbonded pdb=" OG1 THR C 87 " pdb=" OG1 THR D 87 " model vdw 2.099 3.040 nonbonded pdb=" O VAL B 249 " pdb=" OG1 THR B 361 " model vdw 2.141 3.040 nonbonded pdb=" NH1 ARG C 94 " pdb=" O ALA D 132 " model vdw 2.150 3.120 nonbonded pdb=" O LYS B 233 " pdb=" OG1 THR B 236 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 455 " pdb=" OG SER B 459 " model vdw 2.179 3.040 ... (remaining 77362 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 60 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 68 or (resid 69 through 70 and (na \ me N or name CA or name C or name O or name CB )) or resid 71 through 132 or res \ id 134 through 143 or resid 153 through 183 or (resid 184 through 186 and (name \ N or name CA or name C or name O or name CB )) or resid 187 through 198 or resid \ 204 through 217 or (resid 218 through 220 and (name N or name CA or name C or n \ ame O or name CB )) or resid 221 through 242 or (resid 243 and (name N or name C \ A or name C or name O or name CB )) or resid 244 through 351 or resid 353 throug \ h 391 or resid 394 through 399 or (resid 401 and (name N or name CA or name C or \ name O or name CB )) or resid 402 through 407 or (resid 408 through 409 and (na \ me N or name CA or name C or name O or name CB )) or resid 410 through 411 or re \ sid 417 through 418 or (resid 419 and (name N or name CA or name C or name O or \ name CB )) or resid 420 through 495 or (resid 496 through 499 and (name N or nam \ e CA or name C or name O or name CB )) or resid 500 through 507 or (resid 508 an \ d (name N or name CA or name C or name O or name CB )) or resid 509 through 534 \ or (resid 535 through 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 578 or (resid 579 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 588)) selection = (chain 'B' and (resid 60 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 143 or (resid 153 through 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 163 \ or (resid 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 173 or (resid 174 and (name N or name CA or name C or name O or nam \ e CB )) or resid 175 through 185 or (resid 186 and (name N or name CA or name C \ or name O or name CB )) or resid 187 through 274 or (resid 275 and (name N or na \ me CA or name C or name O or name CB )) or resid 276 through 330 or (resid 331 a \ nd (name N or name CA or name C or name O or name CB )) or resid 332 through 382 \ or (resid 383 and (name N or name CA or name C or name O or name CB )) or resid \ 384 through 386 or (resid 387 and (name N or name CA or name C or name O or nam \ e CB )) or resid 388 through 399 or resid 401 through 455 or (resid 456 and (nam \ e N or name CA or name C or name O or name CB )) or resid 457 through 500 or res \ id 503 through 504 or (resid 505 and (name N or name CA or name C or name O or n \ ame CB )) or resid 506 through 518 or (resid 519 and (name N or name CA or name \ C or name O or name CB )) or resid 520 through 536 or (resid 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 552 or (resid 553 \ through 556 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 57 through 573 or (resid 574 and (name N or name CA or name C or name O or name \ CB )) or resid 575 through 582 or (resid 583 and (name N or name CA or name C or \ name O or name CB )) or resid 584 through 588)) } ncs_group { reference = (chain 'C' and (resid 5 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 32 or (resid 33 and (nam \ e N or name CA or name C or name O or name CB )) or resid 34 through 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 40 or (resid 41 and (name N or name CA or name C or name O or name CB )) or re \ sid 42 through 78 or resid 80 through 101 or (resid 102 through 118 and (name N \ or name CA or name C or name O or name CB )) or resid 119 through 162)) selection = (chain 'D' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 102 or resid 116 through 162)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.004 0.090 9965 Z= 0.188 Angle : 0.820 11.905 13571 Z= 0.463 Chirality : 0.046 0.253 1610 Planarity : 0.007 0.144 1717 Dihedral : 13.926 85.934 3431 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.00 (0.23), residues: 1270 helix: 0.24 (0.24), residues: 446 sheet: -0.61 (0.42), residues: 153 loop : -1.31 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 85 TYR 0.014 0.002 TYR A 432 PHE 0.023 0.002 PHE D 125 TRP 0.024 0.002 TRP B 364 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9963) covalent geometry : angle 0.81402 (13567) SS BOND : bond 0.00109 ( 2) SS BOND : angle 5.66298 ( 4) hydrogen bonds : bond 0.19818 ( 398) hydrogen bonds : angle 7.93097 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.7960 (tpt90) cc_final: 0.7752 (tpt-90) REVERT: D 90 MET cc_start: 0.8642 (tpt) cc_final: 0.8415 (tpt) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1094 time to fit residues: 22.4384 Evaluate side-chains 124 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN D 134 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173559 restraints weight = 11461.750| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.35 r_work: 0.3836 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9965 Z= 0.154 Angle : 0.682 9.257 13571 Z= 0.346 Chirality : 0.046 0.190 1610 Planarity : 0.006 0.095 1717 Dihedral : 5.256 28.775 1366 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 1.29 % Allowed : 8.86 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -0.78 (0.23), residues: 1270 helix: 0.55 (0.24), residues: 459 sheet: -0.46 (0.40), residues: 168 loop : -1.32 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 85 TYR 0.013 0.001 TYR C 40 PHE 0.023 0.002 PHE B 79 TRP 0.019 0.002 TRP A 228 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9963) covalent geometry : angle 0.67914 (13567) SS BOND : bond 0.00118 ( 2) SS BOND : angle 3.39169 ( 4) hydrogen bonds : bond 0.04485 ( 398) hydrogen bonds : angle 5.81069 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 469 LYS cc_start: 0.5743 (ttmt) cc_final: 0.4543 (pttm) REVERT: C 94 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8060 (mtp85) outliers start: 13 outliers final: 6 residues processed: 141 average time/residue: 0.1127 time to fit residues: 21.7037 Evaluate side-chains 123 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 126 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173160 restraints weight = 11467.595| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.53 r_work: 0.3821 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9965 Z= 0.137 Angle : 0.637 8.616 13571 Z= 0.324 Chirality : 0.044 0.183 1610 Planarity : 0.005 0.071 1717 Dihedral : 4.996 23.965 1364 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 1.59 % Allowed : 12.05 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -0.78 (0.23), residues: 1270 helix: 0.64 (0.24), residues: 459 sheet: -0.71 (0.38), residues: 178 loop : -1.33 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 85 TYR 0.011 0.001 TYR C 40 PHE 0.020 0.002 PHE B 588 TRP 0.023 0.002 TRP A 228 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9963) covalent geometry : angle 0.63503 (13567) SS BOND : bond 0.00364 ( 2) SS BOND : angle 2.87442 ( 4) hydrogen bonds : bond 0.04057 ( 398) hydrogen bonds : angle 5.31206 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (m-10) outliers start: 16 outliers final: 7 residues processed: 137 average time/residue: 0.1093 time to fit residues: 20.7040 Evaluate side-chains 129 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN B 305 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.198243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166563 restraints weight = 11577.809| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.28 r_work: 0.3733 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9965 Z= 0.233 Angle : 0.704 8.290 13571 Z= 0.360 Chirality : 0.047 0.192 1610 Planarity : 0.005 0.070 1717 Dihedral : 5.229 24.379 1364 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 2.69 % Allowed : 15.24 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.18 (0.22), residues: 1270 helix: 0.21 (0.23), residues: 463 sheet: -0.82 (0.39), residues: 169 loop : -1.51 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 425 TYR 0.013 0.002 TYR B 432 PHE 0.024 0.003 PHE D 67 TRP 0.026 0.003 TRP A 228 HIS 0.019 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 9963) covalent geometry : angle 0.70213 (13567) SS BOND : bond 0.00395 ( 2) SS BOND : angle 3.06273 ( 4) hydrogen bonds : bond 0.04245 ( 398) hydrogen bonds : angle 5.34282 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: C 85 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7587 (mtp-110) REVERT: D 15 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: A 213 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 386 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8595 (mp) outliers start: 27 outliers final: 14 residues processed: 147 average time/residue: 0.1084 time to fit residues: 21.9281 Evaluate side-chains 141 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 104 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.198296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.177916 restraints weight = 10865.561| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.50 r_work: 0.3744 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9965 Z= 0.166 Angle : 0.644 8.920 13571 Z= 0.327 Chirality : 0.045 0.245 1610 Planarity : 0.005 0.061 1717 Dihedral : 5.083 24.874 1364 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 3.39 % Allowed : 15.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.06 (0.23), residues: 1270 helix: 0.39 (0.24), residues: 460 sheet: -0.73 (0.41), residues: 162 loop : -1.52 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 425 TYR 0.009 0.001 TYR C 40 PHE 0.015 0.002 PHE D 67 TRP 0.028 0.002 TRP B 228 HIS 0.011 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9963) covalent geometry : angle 0.64285 (13567) SS BOND : bond 0.00338 ( 2) SS BOND : angle 2.51290 ( 4) hydrogen bonds : bond 0.03863 ( 398) hydrogen bonds : angle 5.10513 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7816 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: B 386 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8669 (mp) REVERT: D 15 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: A 79 PHE cc_start: 0.7725 (m-10) cc_final: 0.7472 (m-10) REVERT: A 120 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8550 (p0) REVERT: A 213 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 386 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8665 (mp) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 0.1078 time to fit residues: 23.4629 Evaluate side-chains 149 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 126 optimal weight: 0.0870 chunk 109 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.198433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177275 restraints weight = 10844.676| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.67 r_work: 0.3741 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9965 Z= 0.157 Angle : 0.634 8.947 13571 Z= 0.323 Chirality : 0.044 0.190 1610 Planarity : 0.005 0.056 1717 Dihedral : 4.989 25.342 1364 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 3.69 % Allowed : 16.73 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.00 (0.23), residues: 1270 helix: 0.47 (0.24), residues: 461 sheet: -0.80 (0.43), residues: 149 loop : -1.47 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 344 TYR 0.011 0.001 TYR A 335 PHE 0.015 0.002 PHE D 67 TRP 0.026 0.002 TRP A 228 HIS 0.009 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9963) covalent geometry : angle 0.63176 (13567) SS BOND : bond 0.00249 ( 2) SS BOND : angle 3.09642 ( 4) hydrogen bonds : bond 0.03755 ( 398) hydrogen bonds : angle 5.00093 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8563 (m) cc_final: 0.8186 (p) REVERT: B 364 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: B 366 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7740 (mtpt) REVERT: D 15 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: A 79 PHE cc_start: 0.7777 (m-10) cc_final: 0.7559 (m-10) REVERT: A 213 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 386 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8665 (mp) outliers start: 37 outliers final: 19 residues processed: 162 average time/residue: 0.1124 time to fit residues: 24.7809 Evaluate side-chains 151 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169946 restraints weight = 10841.231| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.71 r_work: 0.3785 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9965 Z= 0.145 Angle : 0.632 9.242 13571 Z= 0.322 Chirality : 0.044 0.226 1610 Planarity : 0.005 0.055 1717 Dihedral : 4.899 25.508 1364 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 3.49 % Allowed : 16.24 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -0.91 (0.23), residues: 1270 helix: 0.59 (0.24), residues: 461 sheet: -0.85 (0.43), residues: 149 loop : -1.43 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 344 TYR 0.012 0.001 TYR A 109 PHE 0.014 0.002 PHE B 588 TRP 0.027 0.002 TRP A 228 HIS 0.008 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9963) covalent geometry : angle 0.63047 (13567) SS BOND : bond 0.00415 ( 2) SS BOND : angle 2.74152 ( 4) hydrogen bonds : bond 0.03661 ( 398) hydrogen bonds : angle 4.90812 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8572 (m) cc_final: 0.8201 (p) REVERT: B 364 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: B 366 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7743 (mtpt) REVERT: B 467 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: B 486 ILE cc_start: 0.8968 (pt) cc_final: 0.8634 (mt) REVERT: B 541 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7767 (pp) REVERT: D 15 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: A 79 PHE cc_start: 0.7778 (m-10) cc_final: 0.7491 (m-10) REVERT: A 213 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 386 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8650 (mp) outliers start: 35 outliers final: 19 residues processed: 158 average time/residue: 0.1038 time to fit residues: 22.8088 Evaluate side-chains 147 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169168 restraints weight = 10883.642| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.56 r_work: 0.3766 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9965 Z= 0.167 Angle : 0.657 9.687 13571 Z= 0.331 Chirality : 0.046 0.332 1610 Planarity : 0.005 0.055 1717 Dihedral : 4.929 25.708 1364 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 3.39 % Allowed : 16.24 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -0.99 (0.23), residues: 1270 helix: 0.51 (0.24), residues: 460 sheet: -0.90 (0.44), residues: 149 loop : -1.45 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 344 TYR 0.011 0.001 TYR A 335 PHE 0.016 0.002 PHE D 67 TRP 0.030 0.002 TRP A 228 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9963) covalent geometry : angle 0.65568 (13567) SS BOND : bond 0.00456 ( 2) SS BOND : angle 2.75094 ( 4) hydrogen bonds : bond 0.03694 ( 398) hydrogen bonds : angle 4.91774 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 111 SER cc_start: 0.8572 (m) cc_final: 0.8195 (p) REVERT: B 364 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: B 366 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7766 (mtpt) REVERT: B 467 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7354 (t-90) REVERT: B 486 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 541 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7761 (pp) REVERT: C 49 MET cc_start: 0.7659 (tmm) cc_final: 0.7415 (ttp) REVERT: D 15 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: A 79 PHE cc_start: 0.7858 (m-10) cc_final: 0.7597 (m-10) REVERT: A 213 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8035 (mt) REVERT: A 386 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8646 (mp) outliers start: 34 outliers final: 18 residues processed: 150 average time/residue: 0.1000 time to fit residues: 21.0995 Evaluate side-chains 146 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165385 restraints weight = 11008.164| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.66 r_work: 0.3742 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9965 Z= 0.225 Angle : 0.715 10.069 13571 Z= 0.361 Chirality : 0.047 0.213 1610 Planarity : 0.005 0.059 1717 Dihedral : 5.161 26.009 1364 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 2.89 % Allowed : 16.43 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.30 (0.23), residues: 1270 helix: 0.23 (0.24), residues: 462 sheet: -1.27 (0.43), residues: 149 loop : -1.57 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 344 TYR 0.014 0.002 TYR A 211 PHE 0.019 0.002 PHE D 67 TRP 0.035 0.003 TRP A 228 HIS 0.008 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 9963) covalent geometry : angle 0.71345 (13567) SS BOND : bond 0.00548 ( 2) SS BOND : angle 3.07464 ( 4) hydrogen bonds : bond 0.03954 ( 398) hydrogen bonds : angle 5.12803 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 111 SER cc_start: 0.8561 (m) cc_final: 0.8204 (p) REVERT: B 364 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: B 366 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7739 (mtpt) REVERT: B 467 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7354 (t-90) REVERT: B 541 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7835 (pp) REVERT: D 15 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: A 213 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 386 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (mp) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 0.0993 time to fit residues: 20.8038 Evaluate side-chains 146 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 0.0060 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.193563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170830 restraints weight = 10846.296| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.65 r_work: 0.3800 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9965 Z= 0.134 Angle : 0.663 11.229 13571 Z= 0.330 Chirality : 0.044 0.221 1610 Planarity : 0.005 0.060 1717 Dihedral : 4.894 21.846 1364 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 2.59 % Allowed : 17.63 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.07 (0.23), residues: 1270 helix: 0.45 (0.24), residues: 468 sheet: -1.35 (0.43), residues: 141 loop : -1.43 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 85 TYR 0.018 0.001 TYR A 335 PHE 0.014 0.002 PHE B 588 TRP 0.039 0.002 TRP B 228 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9963) covalent geometry : angle 0.66138 (13567) SS BOND : bond 0.00489 ( 2) SS BOND : angle 2.72397 ( 4) hydrogen bonds : bond 0.03555 ( 398) hydrogen bonds : angle 4.90744 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 111 SER cc_start: 0.8501 (m) cc_final: 0.8139 (p) REVERT: B 364 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: B 366 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7769 (mtpt) REVERT: B 467 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7396 (t-90) REVERT: B 486 ILE cc_start: 0.8937 (pt) cc_final: 0.8625 (mt) REVERT: B 541 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7769 (pp) REVERT: C 49 MET cc_start: 0.7644 (tmm) cc_final: 0.7381 (ttp) REVERT: D 15 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: A 213 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 263 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (mt) REVERT: A 357 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7052 (tt) REVERT: A 386 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (mp) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.0941 time to fit residues: 19.4745 Evaluate side-chains 146 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN A 241 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.192495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169266 restraints weight = 10913.847| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.75 r_work: 0.3782 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9965 Z= 0.154 Angle : 0.678 11.970 13571 Z= 0.340 Chirality : 0.045 0.211 1610 Planarity : 0.005 0.069 1717 Dihedral : 4.882 22.996 1364 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 2.69 % Allowed : 17.13 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.03 (0.23), residues: 1270 helix: 0.50 (0.24), residues: 460 sheet: -1.27 (0.42), residues: 151 loop : -1.40 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 344 TYR 0.015 0.001 TYR A 335 PHE 0.017 0.002 PHE B 79 TRP 0.035 0.002 TRP B 228 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9963) covalent geometry : angle 0.67540 (13567) SS BOND : bond 0.00596 ( 2) SS BOND : angle 3.27205 ( 4) hydrogen bonds : bond 0.03556 ( 398) hydrogen bonds : angle 4.91206 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.23 seconds wall clock time: 40 minutes 42.03 seconds (2442.03 seconds total)