Starting phenix.real_space_refine on Fri Feb 14 04:03:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j60_33735/02_2025/8j60_33735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j60_33735/02_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_33735/02_2025/8j60_33735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j60_33735/02_2025/8j60_33735.map" model { file = "/net/cci-nas-00/data/ceres_data/8j60_33735/02_2025/8j60_33735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j60_33735/02_2025/8j60_33735.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 6} 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: {'ARG:plan': 2, 'HIS:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 221 Time building chain proxies: 6.61, per 1000 atoms: 0.68 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.19 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: 3.02 Time building geometry restraints manager: 2.68 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.000 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- 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 9963 Z= 0.276 Angle : 0.814 11.905 13567 Z= 0.461 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP B 364 HIS 0.005 0.001 HIS A 267 PHE 0.023 0.002 PHE D 125 TYR 0.014 0.002 TYR A 432 ARG 0.008 0.001 ARG D 85 *********************** 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 : 1.064 Fit side-chains 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: 0.2493 time to fit residues: 51.5529 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 : 1.114 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.208327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177189 restraints weight = 11432.942| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.34 r_work: 0.3874 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9963 Z= 0.200 Angle : 0.664 9.320 13567 Z= 0.337 Chirality : 0.045 0.184 1610 Planarity : 0.005 0.093 1717 Dihedral : 5.173 28.184 1366 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 1.29 % Allowed : 8.57 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1270 helix: 0.71 (0.24), residues: 458 sheet: -0.38 (0.40), residues: 168 loop : -1.29 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 228 HIS 0.006 0.001 HIS A 267 PHE 0.022 0.002 PHE B 79 TYR 0.012 0.001 TYR C 40 ARG 0.007 0.001 ARG D 85 *********************** 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 152 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8395 (p0) REVERT: A 352 LEU cc_start: 0.4777 (tt) cc_final: 0.4572 (mt) outliers start: 13 outliers final: 7 residues processed: 146 average time/residue: 0.2469 time to fit residues: 49.6771 Evaluate side-chains 122 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 GLU 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 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 79 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.206053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173831 restraints weight = 11551.145| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.55 r_work: 0.3826 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9963 Z= 0.212 Angle : 0.628 7.884 13567 Z= 0.319 Chirality : 0.044 0.186 1610 Planarity : 0.005 0.072 1717 Dihedral : 4.993 23.940 1366 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 1.89 % Allowed : 11.85 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1270 helix: 0.71 (0.24), residues: 459 sheet: -0.49 (0.40), residues: 164 loop : -1.30 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 228 HIS 0.004 0.001 HIS A 267 PHE 0.020 0.002 PHE B 588 TYR 0.011 0.001 TYR C 40 ARG 0.004 0.001 ARG D 85 *********************** 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 145 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 366 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7676 (mtpt) outliers start: 19 outliers final: 8 residues processed: 133 average time/residue: 0.2475 time to fit residues: 45.3021 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS 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 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.202297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171227 restraints weight = 11358.841| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.47 r_work: 0.3800 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9963 Z= 0.250 Angle : 0.638 7.919 13567 Z= 0.324 Chirality : 0.045 0.182 1610 Planarity : 0.005 0.065 1717 Dihedral : 4.938 24.500 1364 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 2.69 % Allowed : 14.24 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1270 helix: 0.64 (0.24), residues: 458 sheet: -0.49 (0.41), residues: 163 loop : -1.38 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 228 HIS 0.015 0.001 HIS A 384 PHE 0.020 0.002 PHE D 67 TYR 0.010 0.001 TYR C 40 ARG 0.006 0.001 ARG C 94 *********************** 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 161 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8558 (m) cc_final: 0.8221 (p) REVERT: B 366 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7685 (mtpt) REVERT: C 85 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7507 (mtp-110) REVERT: D 15 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: A 213 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 386 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 525 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7861 (mtp85) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.2409 time to fit residues: 49.4578 Evaluate side-chains 141 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 567 ILE 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 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 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 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 101 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 127 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.203582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170887 restraints weight = 11309.316| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.59 r_work: 0.3811 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9963 Z= 0.192 Angle : 0.600 7.661 13567 Z= 0.305 Chirality : 0.043 0.222 1610 Planarity : 0.005 0.055 1717 Dihedral : 4.776 24.582 1364 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 2.89 % Allowed : 14.84 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1270 helix: 0.75 (0.24), residues: 463 sheet: -0.60 (0.40), residues: 171 loop : -1.35 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 228 HIS 0.011 0.001 HIS A 384 PHE 0.017 0.002 PHE A 118 TYR 0.008 0.001 TYR A 335 ARG 0.006 0.001 ARG C 94 *********************** 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 161 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8572 (m) cc_final: 0.8230 (p) REVERT: B 364 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.7337 (m-10) REVERT: B 366 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7687 (mtpt) REVERT: B 466 THR cc_start: 0.8136 (t) cc_final: 0.7747 (m) REVERT: C 85 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7544 (mtp-110) REVERT: A 213 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 386 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 525 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7923 (mtp85) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 0.2502 time to fit residues: 51.1475 Evaluate side-chains 142 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS 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 529 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain D residue 23 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 98 optimal weight: 0.0670 chunk 110 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 13 optimal weight: 0.0170 chunk 28 optimal weight: 5.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 341 GLN ** 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 = 0.4305 r_free = 0.4305 target = 0.204344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171964 restraints weight = 11400.551| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.67 r_work: 0.3817 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9963 Z= 0.175 Angle : 0.593 9.169 13567 Z= 0.300 Chirality : 0.043 0.172 1610 Planarity : 0.004 0.054 1717 Dihedral : 4.641 25.041 1364 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 2.79 % Allowed : 16.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1270 helix: 0.87 (0.24), residues: 465 sheet: -0.58 (0.40), residues: 171 loop : -1.29 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 228 HIS 0.008 0.001 HIS A 384 PHE 0.015 0.002 PHE A 118 TYR 0.010 0.001 TYR A 335 ARG 0.006 0.001 ARG B 425 *********************** 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 159 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8565 (m) cc_final: 0.8232 (p) REVERT: B 364 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: B 366 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7738 (mtpt) REVERT: C 85 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7523 (mtp-110) REVERT: D 15 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: A 213 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 386 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 570 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7896 (tt) outliers start: 28 outliers final: 17 residues processed: 150 average time/residue: 0.2358 time to fit residues: 49.1129 Evaluate side-chains 143 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS 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 529 VAL Chi-restraints excluded: chain B residue 567 ILE 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 124 LEU 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 117 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 105 optimal weight: 0.0370 overall best weight: 1.2072 ------------------------------------------------------------------------------- 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 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 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN A 467 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.192268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168110 restraints weight = 10943.395| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.75 r_work: 0.3745 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9963 Z= 0.313 Angle : 0.658 9.349 13567 Z= 0.336 Chirality : 0.045 0.191 1610 Planarity : 0.005 0.055 1717 Dihedral : 4.905 26.000 1364 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 2.69 % Allowed : 16.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1270 helix: 0.57 (0.24), residues: 456 sheet: -0.90 (0.42), residues: 155 loop : -1.34 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 228 HIS 0.009 0.001 HIS A 384 PHE 0.023 0.002 PHE D 67 TYR 0.011 0.002 TYR A 211 ARG 0.007 0.001 ARG B 425 *********************** 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 161 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: B 111 SER cc_start: 0.8569 (m) cc_final: 0.8234 (p) REVERT: B 364 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: B 366 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7780 (mtpt) REVERT: B 467 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7419 (t-90) REVERT: C 85 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7680 (mtp-110) REVERT: D 15 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: A 79 PHE cc_start: 0.7879 (m-10) cc_final: 0.7569 (m-10) REVERT: A 120 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8680 (p0) REVERT: A 213 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 386 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (mp) outliers start: 27 outliers final: 18 residues processed: 153 average time/residue: 0.2368 time to fit residues: 50.1442 Evaluate side-chains 148 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain D residue 15 GLU 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 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 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 73 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.199846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178677 restraints weight = 10750.642| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.79 r_work: 0.3741 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9963 Z= 0.251 Angle : 0.647 9.966 13567 Z= 0.327 Chirality : 0.044 0.177 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.849 25.922 1364 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 3.19 % Allowed : 16.93 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1270 helix: 0.63 (0.24), residues: 457 sheet: -0.78 (0.40), residues: 164 loop : -1.40 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 228 HIS 0.008 0.001 HIS A 384 PHE 0.015 0.002 PHE D 67 TYR 0.009 0.001 TYR A 335 ARG 0.009 0.001 ARG B 425 *********************** 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 167 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8584 (m) cc_final: 0.8224 (p) REVERT: B 364 TRP cc_start: 0.7981 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: B 366 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7835 (mtpt) REVERT: B 467 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7381 (t-90) REVERT: D 15 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: A 79 PHE cc_start: 0.7874 (m-10) cc_final: 0.7660 (m-10) REVERT: A 213 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 337 LEU cc_start: 0.8471 (tt) cc_final: 0.8271 (tp) REVERT: A 386 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8636 (mp) outliers start: 32 outliers final: 19 residues processed: 157 average time/residue: 0.2387 time to fit residues: 51.6047 Evaluate side-chains 148 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS 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 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 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 313 THR Chi-restraints excluded: chain A residue 320 CYS 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 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.0670 chunk 95 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 275 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 = 0.4164 r_free = 0.4164 target = 0.195279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171849 restraints weight = 10848.845| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.77 r_work: 0.3781 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9963 Z= 0.203 Angle : 0.632 9.808 13567 Z= 0.318 Chirality : 0.043 0.177 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.738 21.602 1364 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 2.79 % Allowed : 17.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1270 helix: 0.73 (0.24), residues: 463 sheet: -0.91 (0.39), residues: 170 loop : -1.34 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 228 HIS 0.008 0.001 HIS A 384 PHE 0.015 0.002 PHE B 79 TYR 0.013 0.001 TYR A 335 ARG 0.015 0.001 ARG A 344 *********************** 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 153 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8565 (m) cc_final: 0.8192 (p) REVERT: B 364 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: B 366 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7819 (mtpt) REVERT: B 467 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7397 (t-90) REVERT: B 486 ILE cc_start: 0.8926 (pt) cc_final: 0.8550 (mt) REVERT: B 541 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7757 (pp) REVERT: D 15 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: A 213 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 386 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8648 (mp) outliers start: 28 outliers final: 19 residues processed: 144 average time/residue: 0.2232 time to fit residues: 45.6942 Evaluate side-chains 144 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 HIS 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 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 313 THR Chi-restraints excluded: chain A residue 320 CYS 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 465 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 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4159 r_free = 0.4159 target = 0.194755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.171400 restraints weight = 10881.987| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.82 r_work: 0.3798 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9963 Z= 0.222 Angle : 0.633 9.865 13567 Z= 0.320 Chirality : 0.044 0.176 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.708 21.809 1364 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 2.69 % Allowed : 17.33 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1270 helix: 0.71 (0.24), residues: 463 sheet: -0.98 (0.39), residues: 170 loop : -1.34 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 228 HIS 0.007 0.001 HIS A 384 PHE 0.020 0.002 PHE B 79 TYR 0.010 0.001 TYR A 335 ARG 0.012 0.001 ARG C 85 ********************** 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 150 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 SER cc_start: 0.8526 (m) cc_final: 0.8180 (p) REVERT: B 364 TRP cc_start: 0.7891 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: B 366 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7816 (mtpt) REVERT: B 467 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7424 (t-90) REVERT: B 486 ILE cc_start: 0.8927 (pt) cc_final: 0.8583 (mt) REVERT: B 541 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7744 (pp) REVERT: C 49 MET cc_start: 0.7673 (tmm) cc_final: 0.7389 (ttp) REVERT: D 15 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: A 184 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.6224 (p-90) REVERT: A 213 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7944 (mt) REVERT: A 344 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6720 (mtm-85) REVERT: A 386 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8655 (mp) outliers start: 27 outliers final: 19 residues processed: 139 average time/residue: 0.2272 time to fit residues: 44.0209 Evaluate side-chains 146 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 GLU 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 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 184 TRP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 320 CYS 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 465 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 102 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.0070 chunk 114 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 275 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.195830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172624 restraints weight = 10799.515| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.75 r_work: 0.3806 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9963 Z= 0.195 Angle : 0.630 9.865 13567 Z= 0.316 Chirality : 0.043 0.176 1610 Planarity : 0.005 0.053 1717 Dihedral : 4.627 21.598 1364 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 17.53 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1270 helix: 0.79 (0.24), residues: 463 sheet: -1.05 (0.41), residues: 157 loop : -1.28 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 228 HIS 0.007 0.001 HIS A 384 PHE 0.014 0.002 PHE A 79 TYR 0.012 0.001 TYR A 335 ARG 0.010 0.001 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.71 seconds wall clock time: 83 minutes 0.76 seconds (4980.76 seconds total)