Starting phenix.real_space_refine on Wed Sep 17 20:17:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc4_70308/09_2025/9oc4_70308.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 5 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 7077 2.51 5 N 1837 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 11068 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5064 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 26, 'TRANS': 654} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1417 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' K': 1, '9Y0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 76 Unusual residues: {' K': 1, ' MG': 2, '9Y0': 1, 'ADP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 3.29, per 1000 atoms: 0.30 Number of scatterers: 11068 At special positions: 0 Unit cell: (133.92, 81.84, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 61 16.00 P 5 15.00 Mg 2 11.99 O 2084 8.00 N 1837 7.00 C 7077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 191 " 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: 1.01 Conformation dependent library (CDL) restraints added in 585.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 65.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.513A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.801A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.763A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 275 removed outlier: 4.533A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.538A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.042A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.268A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.224A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.633A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.733A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.494A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.627A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.688A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.543A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.894A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 removed outlier: 3.511A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 24 removed outlier: 3.508A pdb=" N VAL B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.672A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 99 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.683A pdb=" N VAL B 207 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.707A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 4.781A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.689A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.504A pdb=" N LYS B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.128A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.528A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.592A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.572A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.659A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.541A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.127A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 657 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.830A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.501A pdb=" N THR C 122 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.835A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 removed outlier: 3.635A pdb=" N LEU D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.627A pdb=" N LYS B 108 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE B 131 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.107A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 535 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 512 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 303 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 319 removed outlier: 7.173A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.699A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.503A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2056 1.33 - 1.45: 2558 1.45 - 1.57: 6443 1.57 - 1.70: 7 1.70 - 1.82: 111 Bond restraints: 11175 Sorted by residual: bond pdb=" CG PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 1.503 1.294 0.209 3.40e-02 8.65e+02 3.79e+01 bond pdb=" N ILE B 312 " pdb=" CA ILE B 312 " ideal model delta sigma weight residual 1.460 1.495 -0.034 1.19e-02 7.06e+03 8.37e+00 bond pdb=" N GLN B 5 " pdb=" CA GLN B 5 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.23e+00 bond pdb=" N LYS B 4 " pdb=" CA LYS B 4 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" N THR B 311 " pdb=" CA THR B 311 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.90e+00 ... (remaining 11170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 15102 2.95 - 5.89: 75 5.89 - 8.84: 12 8.84 - 11.79: 1 11.79 - 14.73: 1 Bond angle restraints: 15191 Sorted by residual: angle pdb=" N PRO B 524 " pdb=" CD PRO B 524 " pdb=" CG PRO B 524 " ideal model delta sigma weight residual 103.20 88.47 14.73 1.50e+00 4.44e-01 9.65e+01 angle pdb=" N LEU B 8 " pdb=" CA LEU B 8 " pdb=" C LEU B 8 " ideal model delta sigma weight residual 113.12 105.84 7.28 1.25e+00 6.40e-01 3.39e+01 angle pdb=" CA PRO B 524 " pdb=" CB PRO B 524 " pdb=" CG PRO B 524 " ideal model delta sigma weight residual 104.50 93.80 10.70 1.90e+00 2.77e-01 3.17e+01 angle pdb=" CA PRO B 524 " pdb=" N PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 108.30 4.66 1.00e+00 1.00e+00 2.17e+01 ... (remaining 15186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5815 17.44 - 34.87: 645 34.87 - 52.31: 137 52.31 - 69.74: 55 69.74 - 87.18: 16 Dihedral angle restraints: 6668 sinusoidal: 2547 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS B 142 " pdb=" SG CYS B 142 " pdb=" SG CYS B 191 " pdb=" CB CYS B 191 " ideal model delta sinusoidal sigma weight residual 93.00 179.76 -86.76 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU B 183 " pdb=" C LEU B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta harmonic sigma weight residual 180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 6665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1544 0.053 - 0.105: 240 0.105 - 0.158: 32 0.158 - 0.210: 2 0.210 - 0.263: 1 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 4 " pdb=" N LYS B 4 " pdb=" C LYS B 4 " pdb=" CB LYS B 4 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE B 312 " pdb=" N ILE B 312 " pdb=" C ILE B 312 " pdb=" CB ILE B 312 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 1816 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 3 " -0.381 9.50e-02 1.11e+02 1.71e-01 1.80e+01 pdb=" NE ARG B 3 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 3 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 3 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 3 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " -0.037 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 524 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO C 134 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.026 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.66: 172 2.66 - 3.28: 12142 3.28 - 3.90: 23587 3.90 - 4.52: 31837 4.52 - 5.14: 47898 Nonbonded interactions: 115636 Sorted by model distance: nonbonded pdb=" O1B ADP B 702 " pdb="MG MG B 703 " model vdw 2.036 2.170 nonbonded pdb=" NH2 ARG B 3 " pdb=" OD2 ASP B 552 " model vdw 2.064 3.120 nonbonded pdb=" O2A ADP B 702 " pdb="MG MG B 705 " model vdw 2.191 2.170 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.204 3.040 nonbonded pdb=" O ILE C 159 " pdb=" OG SER C 163 " model vdw 2.271 3.040 ... (remaining 115631 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.690 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.003 0.209 11176 Z= 0.142 Angle : 0.556 14.733 15193 Z= 0.306 Chirality : 0.038 0.263 1819 Planarity : 0.005 0.171 1916 Dihedral : 16.365 87.177 4017 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.79 % Allowed : 15.80 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.22), residues: 1444 helix: 1.17 (0.18), residues: 865 sheet: -0.02 (0.58), residues: 84 loop : 0.09 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 3 TYR 0.018 0.001 TYR A 381 PHE 0.006 0.001 PHE B 242 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00312 (11175) covalent geometry : angle 0.55584 (15191) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.14080 ( 2) hydrogen bonds : bond 0.21901 ( 691) hydrogen bonds : angle 7.01162 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.440 Fit side-chains REVERT: B 98 LYS cc_start: 0.7083 (mttt) cc_final: 0.6697 (mttp) REVERT: B 107 ARG cc_start: 0.6141 (mtt180) cc_final: 0.5803 (mtt180) REVERT: B 148 GLU cc_start: 0.7849 (tt0) cc_final: 0.6788 (tm-30) REVERT: B 202 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6842 (ttp80) REVERT: B 316 ASN cc_start: 0.7531 (t0) cc_final: 0.7258 (t0) REVERT: B 338 GLN cc_start: 0.6132 (mt0) cc_final: 0.5916 (mt0) REVERT: B 392 MET cc_start: 0.4498 (ttp) cc_final: 0.3706 (tpt) REVERT: B 446 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7392 (mmmt) outliers start: 9 outliers final: 6 residues processed: 164 average time/residue: 0.6700 time to fit residues: 117.6084 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 563 HIS C 135 GLN C 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101126 restraints weight = 9167.546| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.78 r_work: 0.2984 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11176 Z= 0.189 Angle : 0.631 7.108 15193 Z= 0.330 Chirality : 0.044 0.167 1819 Planarity : 0.005 0.044 1916 Dihedral : 8.949 103.850 1631 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 2.55 % Allowed : 13.26 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.38 (0.22), residues: 1444 helix: 1.54 (0.17), residues: 866 sheet: -0.06 (0.54), residues: 81 loop : 0.10 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 572 TYR 0.022 0.003 TYR A 381 PHE 0.020 0.002 PHE A 527 TRP 0.012 0.002 TRP B 71 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00410 (11175) covalent geometry : angle 0.63064 (15191) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.46051 ( 2) hydrogen bonds : bond 0.06571 ( 691) hydrogen bonds : angle 4.89304 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.466 Fit side-chains REVERT: A 306 ASN cc_start: 0.9038 (t0) cc_final: 0.8718 (t0) REVERT: B 107 ARG cc_start: 0.5715 (mtt180) cc_final: 0.5321 (mtt180) REVERT: B 148 GLU cc_start: 0.7442 (tt0) cc_final: 0.6002 (tm-30) REVERT: B 175 SER cc_start: 0.7640 (m) cc_final: 0.7290 (t) REVERT: B 202 ARG cc_start: 0.6840 (ttt180) cc_final: 0.6502 (ttp80) REVERT: B 316 ASN cc_start: 0.7160 (t0) cc_final: 0.6950 (t0) REVERT: B 338 GLN cc_start: 0.6168 (mt0) cc_final: 0.5936 (mt0) REVERT: B 361 ASN cc_start: 0.6569 (OUTLIER) cc_final: 0.6077 (m-40) REVERT: B 383 MET cc_start: 0.7488 (ptm) cc_final: 0.6975 (ptm) REVERT: B 392 MET cc_start: 0.4126 (ttp) cc_final: 0.3271 (tpt) REVERT: B 446 LYS cc_start: 0.7252 (mmtp) cc_final: 0.6948 (mmmt) outliers start: 29 outliers final: 12 residues processed: 172 average time/residue: 0.6806 time to fit residues: 125.4766 Evaluate side-chains 158 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 135 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 157 GLN C 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104752 restraints weight = 9239.536| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.86 r_work: 0.3020 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11176 Z= 0.124 Angle : 0.527 6.549 15193 Z= 0.273 Chirality : 0.040 0.157 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.594 106.418 1628 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 14.22 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.22), residues: 1444 helix: 1.83 (0.17), residues: 875 sheet: -0.25 (0.52), residues: 81 loop : -0.00 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 181 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE A 109 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00247 (11175) covalent geometry : angle 0.52693 (15191) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.39668 ( 2) hydrogen bonds : bond 0.05260 ( 691) hydrogen bonds : angle 4.55723 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8326 (ttt-90) REVERT: A 205 ASN cc_start: 0.8596 (m-40) cc_final: 0.7893 (t0) REVERT: A 306 ASN cc_start: 0.9070 (t0) cc_final: 0.8812 (t0) REVERT: A 389 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 107 ARG cc_start: 0.5655 (mtt180) cc_final: 0.5194 (mtt180) REVERT: B 110 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4397 (mtt-85) REVERT: B 145 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6628 (mm-30) REVERT: B 148 GLU cc_start: 0.7301 (tt0) cc_final: 0.6007 (tm-30) REVERT: B 175 SER cc_start: 0.7619 (m) cc_final: 0.7332 (t) REVERT: B 202 ARG cc_start: 0.6732 (ttt180) cc_final: 0.6486 (ttp80) REVERT: B 316 ASN cc_start: 0.7193 (t0) cc_final: 0.6993 (t0) REVERT: B 361 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6065 (m-40) REVERT: B 383 MET cc_start: 0.7495 (ptm) cc_final: 0.6951 (ptm) REVERT: B 392 MET cc_start: 0.4473 (ttp) cc_final: 0.3457 (tpt) REVERT: B 446 LYS cc_start: 0.7277 (mmtp) cc_final: 0.6996 (mmmt) outliers start: 27 outliers final: 13 residues processed: 168 average time/residue: 0.6970 time to fit residues: 125.3645 Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 154 GLN C 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100686 restraints weight = 9195.677| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.72 r_work: 0.2940 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11176 Z= 0.198 Angle : 0.627 7.308 15193 Z= 0.327 Chirality : 0.045 0.173 1819 Planarity : 0.005 0.047 1916 Dihedral : 9.147 120.232 1628 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.90 % Allowed : 13.87 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.36 (0.21), residues: 1444 helix: 1.61 (0.17), residues: 862 sheet: -0.41 (0.50), residues: 91 loop : 0.02 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 572 TYR 0.021 0.003 TYR A 381 PHE 0.021 0.002 PHE A 527 TRP 0.012 0.002 TRP B 71 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00434 (11175) covalent geometry : angle 0.62727 (15191) SS BOND : bond 0.00268 ( 1) SS BOND : angle 0.62970 ( 2) hydrogen bonds : bond 0.06408 ( 691) hydrogen bonds : angle 4.75900 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7907 (t) cc_final: 0.7593 (m) REVERT: A 389 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 414 MET cc_start: 0.8727 (mmp) cc_final: 0.8500 (mmm) REVERT: B 107 ARG cc_start: 0.5793 (mtt180) cc_final: 0.5446 (mtt180) REVERT: B 110 ARG cc_start: 0.4688 (OUTLIER) cc_final: 0.3771 (tpp80) REVERT: B 145 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6555 (mm-30) REVERT: B 148 GLU cc_start: 0.7405 (tt0) cc_final: 0.6115 (tm-30) REVERT: B 161 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5857 (mm-30) REVERT: B 175 SER cc_start: 0.7606 (m) cc_final: 0.7136 (m) REVERT: B 202 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6506 (ttp80) REVERT: B 213 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6413 (mpp-170) REVERT: B 316 ASN cc_start: 0.7245 (t0) cc_final: 0.7035 (t0) REVERT: B 383 MET cc_start: 0.7508 (ptm) cc_final: 0.7029 (ptm) REVERT: B 392 MET cc_start: 0.4549 (ttp) cc_final: 0.3525 (tpt) REVERT: B 446 LYS cc_start: 0.7296 (mmtp) cc_final: 0.7041 (mmmt) outliers start: 33 outliers final: 19 residues processed: 164 average time/residue: 0.7281 time to fit residues: 127.5001 Evaluate side-chains 166 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101904 restraints weight = 9213.203| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.72 r_work: 0.2987 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11176 Z= 0.153 Angle : 0.568 7.018 15193 Z= 0.295 Chirality : 0.042 0.165 1819 Planarity : 0.004 0.046 1916 Dihedral : 8.989 123.977 1628 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.72 % Allowed : 14.22 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.22), residues: 1444 helix: 1.74 (0.17), residues: 856 sheet: -0.58 (0.51), residues: 92 loop : -0.06 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.024 0.002 TYR A 381 PHE 0.017 0.002 PHE A 527 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00323 (11175) covalent geometry : angle 0.56782 (15191) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.51017 ( 2) hydrogen bonds : bond 0.05700 ( 691) hydrogen bonds : angle 4.61319 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7898 (t) cc_final: 0.7557 (m) REVERT: A 306 ASN cc_start: 0.9194 (t0) cc_final: 0.8975 (t0) REVERT: A 389 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8665 (mp) REVERT: A 414 MET cc_start: 0.8735 (mmp) cc_final: 0.8493 (mmm) REVERT: B 110 ARG cc_start: 0.4569 (OUTLIER) cc_final: 0.4254 (mtt-85) REVERT: B 145 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: B 148 GLU cc_start: 0.7392 (tt0) cc_final: 0.6126 (tm-30) REVERT: B 175 SER cc_start: 0.7578 (m) cc_final: 0.7131 (m) REVERT: B 202 ARG cc_start: 0.6855 (ttt180) cc_final: 0.6518 (ttp80) REVERT: B 383 MET cc_start: 0.7512 (ptm) cc_final: 0.7021 (ptm) REVERT: B 392 MET cc_start: 0.4568 (ttp) cc_final: 0.3417 (tpt) REVERT: B 446 LYS cc_start: 0.7317 (mmtp) cc_final: 0.7090 (mmmt) REVERT: B 497 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: C 135 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8184 (pm20) outliers start: 31 outliers final: 18 residues processed: 164 average time/residue: 0.6715 time to fit residues: 117.9611 Evaluate side-chains 165 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101980 restraints weight = 9273.717| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.66 r_work: 0.2980 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11176 Z= 0.145 Angle : 0.559 6.884 15193 Z= 0.290 Chirality : 0.041 0.164 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.892 125.356 1628 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.37 % Allowed : 14.66 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1444 helix: 1.77 (0.17), residues: 863 sheet: -0.62 (0.51), residues: 92 loop : -0.16 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.023 0.002 TYR A 381 PHE 0.016 0.002 PHE A 527 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00303 (11175) covalent geometry : angle 0.55851 (15191) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.46924 ( 2) hydrogen bonds : bond 0.05523 ( 691) hydrogen bonds : angle 4.55194 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7899 (t) cc_final: 0.7547 (m) REVERT: A 205 ASN cc_start: 0.8598 (m-40) cc_final: 0.7922 (t0) REVERT: A 306 ASN cc_start: 0.9186 (t0) cc_final: 0.8921 (t0) REVERT: A 389 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8676 (mp) REVERT: B 110 ARG cc_start: 0.4408 (OUTLIER) cc_final: 0.3837 (mpt90) REVERT: B 145 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: B 148 GLU cc_start: 0.7351 (tt0) cc_final: 0.6103 (tm-30) REVERT: B 175 SER cc_start: 0.7566 (m) cc_final: 0.7162 (m) REVERT: B 181 ARG cc_start: 0.6443 (mmm-85) cc_final: 0.6075 (ttp80) REVERT: B 202 ARG cc_start: 0.6845 (ttt180) cc_final: 0.6532 (ttp80) REVERT: B 213 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6292 (mpp-170) REVERT: B 383 MET cc_start: 0.7505 (ptm) cc_final: 0.7028 (ptm) REVERT: B 392 MET cc_start: 0.4549 (ttp) cc_final: 0.3382 (tpt) REVERT: B 446 LYS cc_start: 0.7316 (mmtp) cc_final: 0.7050 (mmmt) REVERT: B 497 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6453 (mp0) outliers start: 27 outliers final: 17 residues processed: 159 average time/residue: 0.7041 time to fit residues: 119.9325 Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN C 135 GLN C 154 GLN C 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102477 restraints weight = 9154.122| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.67 r_work: 0.2993 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11176 Z= 0.142 Angle : 0.554 6.872 15193 Z= 0.287 Chirality : 0.041 0.164 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.814 126.730 1628 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.90 % Allowed : 14.14 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1444 helix: 1.81 (0.17), residues: 866 sheet: -0.62 (0.51), residues: 92 loop : -0.15 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.023 0.002 TYR A 381 PHE 0.016 0.001 PHE A 527 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00298 (11175) covalent geometry : angle 0.55407 (15191) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.48768 ( 2) hydrogen bonds : bond 0.05457 ( 691) hydrogen bonds : angle 4.51268 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7888 (t) cc_final: 0.7515 (m) REVERT: A 205 ASN cc_start: 0.8608 (m-40) cc_final: 0.7907 (t0) REVERT: A 306 ASN cc_start: 0.9154 (t0) cc_final: 0.8877 (t0) REVERT: A 389 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8666 (mp) REVERT: B 110 ARG cc_start: 0.4482 (OUTLIER) cc_final: 0.3944 (mpt90) REVERT: B 145 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6611 (mm-30) REVERT: B 148 GLU cc_start: 0.7391 (tt0) cc_final: 0.6134 (tm-30) REVERT: B 175 SER cc_start: 0.7544 (m) cc_final: 0.7161 (m) REVERT: B 181 ARG cc_start: 0.6419 (mmm-85) cc_final: 0.6070 (ttp80) REVERT: B 202 ARG cc_start: 0.6769 (ttt180) cc_final: 0.6512 (ttp80) REVERT: B 213 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6323 (mpp-170) REVERT: B 383 MET cc_start: 0.7497 (ptm) cc_final: 0.7005 (ptm) REVERT: B 392 MET cc_start: 0.4537 (ttp) cc_final: 0.3380 (tpt) REVERT: B 446 LYS cc_start: 0.7321 (mmtp) cc_final: 0.7070 (mmmt) REVERT: B 497 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6418 (mp0) outliers start: 33 outliers final: 20 residues processed: 166 average time/residue: 0.6921 time to fit residues: 122.8798 Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 11 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN C 135 GLN C 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101795 restraints weight = 9174.109| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.84 r_work: 0.2981 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11176 Z= 0.151 Angle : 0.567 6.979 15193 Z= 0.294 Chirality : 0.042 0.166 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.839 127.405 1628 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.72 % Allowed : 14.75 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.21), residues: 1444 helix: 1.81 (0.17), residues: 862 sheet: -0.65 (0.50), residues: 92 loop : -0.17 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.023 0.002 TYR A 381 PHE 0.017 0.002 PHE A 527 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00320 (11175) covalent geometry : angle 0.56742 (15191) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.49364 ( 2) hydrogen bonds : bond 0.05575 ( 691) hydrogen bonds : angle 4.55326 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7906 (t) cc_final: 0.7526 (m) REVERT: A 205 ASN cc_start: 0.8650 (m-40) cc_final: 0.7933 (t0) REVERT: A 306 ASN cc_start: 0.9185 (t0) cc_final: 0.8923 (t0) REVERT: A 389 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 110 ARG cc_start: 0.4543 (OUTLIER) cc_final: 0.3956 (mpt90) REVERT: B 145 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6610 (mm-30) REVERT: B 148 GLU cc_start: 0.7399 (tt0) cc_final: 0.6135 (tm-30) REVERT: B 175 SER cc_start: 0.7531 (m) cc_final: 0.7147 (m) REVERT: B 181 ARG cc_start: 0.6374 (mmm-85) cc_final: 0.6076 (ttp80) REVERT: B 213 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6349 (mpp-170) REVERT: B 383 MET cc_start: 0.7499 (ptm) cc_final: 0.7019 (ptm) REVERT: B 392 MET cc_start: 0.4541 (ttp) cc_final: 0.3382 (tpt) REVERT: B 446 LYS cc_start: 0.7304 (mmtp) cc_final: 0.7061 (mmmt) REVERT: B 497 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: C 135 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (pm20) outliers start: 31 outliers final: 19 residues processed: 162 average time/residue: 0.6998 time to fit residues: 121.3236 Evaluate side-chains 165 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103039 restraints weight = 9153.874| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.68 r_work: 0.3001 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11176 Z= 0.131 Angle : 0.538 6.732 15193 Z= 0.279 Chirality : 0.040 0.162 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.702 127.117 1628 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.37 % Allowed : 15.28 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.22), residues: 1444 helix: 1.89 (0.17), residues: 876 sheet: -0.61 (0.52), residues: 87 loop : -0.15 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.023 0.002 TYR A 381 PHE 0.013 0.001 PHE A 527 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00268 (11175) covalent geometry : angle 0.53790 (15191) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.43297 ( 2) hydrogen bonds : bond 0.05173 ( 691) hydrogen bonds : angle 4.46627 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7876 (t) cc_final: 0.7496 (m) REVERT: A 205 ASN cc_start: 0.8635 (m-40) cc_final: 0.7923 (t0) REVERT: A 306 ASN cc_start: 0.9128 (t0) cc_final: 0.8892 (t0) REVERT: A 389 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8663 (mp) REVERT: B 110 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.3932 (mpt90) REVERT: B 121 VAL cc_start: 0.5223 (OUTLIER) cc_final: 0.4854 (p) REVERT: B 145 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6564 (mm-30) REVERT: B 148 GLU cc_start: 0.7400 (tt0) cc_final: 0.6054 (tm-30) REVERT: B 175 SER cc_start: 0.7511 (m) cc_final: 0.7124 (m) REVERT: B 181 ARG cc_start: 0.6351 (mmm-85) cc_final: 0.6063 (ttp80) REVERT: B 213 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6290 (mpp-170) REVERT: B 383 MET cc_start: 0.7480 (ptm) cc_final: 0.6979 (ptm) REVERT: B 392 MET cc_start: 0.4511 (ttp) cc_final: 0.3315 (tpt) REVERT: B 446 LYS cc_start: 0.7329 (mmtp) cc_final: 0.7073 (mmmt) REVERT: B 497 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: C 135 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8116 (pm20) outliers start: 27 outliers final: 16 residues processed: 161 average time/residue: 0.6724 time to fit residues: 115.8700 Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 0.0970 chunk 100 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN C 135 GLN C 154 GLN C 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104600 restraints weight = 9292.608| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.63 r_work: 0.3034 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.002 0.037 11176 Z= 0.112 Angle : 0.510 6.538 15193 Z= 0.263 Chirality : 0.039 0.157 1819 Planarity : 0.004 0.045 1916 Dihedral : 8.430 125.456 1628 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.93 % Allowed : 15.54 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.22), residues: 1444 helix: 2.02 (0.17), residues: 877 sheet: -0.61 (0.52), residues: 87 loop : -0.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.023 0.001 TYR A 381 PHE 0.010 0.001 PHE A 109 TRP 0.013 0.001 TRP B 71 HIS 0.001 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00220 (11175) covalent geometry : angle 0.50962 (15191) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.35966 ( 2) hydrogen bonds : bond 0.04665 ( 691) hydrogen bonds : angle 4.33350 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8301 (ttt180) REVERT: A 48 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7605 (ttp80) REVERT: A 205 ASN cc_start: 0.8628 (m-40) cc_final: 0.7901 (t0) REVERT: A 306 ASN cc_start: 0.9075 (t0) cc_final: 0.8795 (t0) REVERT: A 389 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8667 (mp) REVERT: B 110 ARG cc_start: 0.4533 (OUTLIER) cc_final: 0.4018 (mpt90) REVERT: B 145 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: B 148 GLU cc_start: 0.7466 (tt0) cc_final: 0.6137 (tm-30) REVERT: B 175 SER cc_start: 0.7459 (m) cc_final: 0.7096 (m) REVERT: B 181 ARG cc_start: 0.6349 (mmm-85) cc_final: 0.6053 (ttp80) REVERT: B 213 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6284 (mpp-170) REVERT: B 383 MET cc_start: 0.7479 (ptm) cc_final: 0.6949 (ptm) REVERT: B 392 MET cc_start: 0.4529 (ttp) cc_final: 0.3333 (tpt) REVERT: B 446 LYS cc_start: 0.7340 (mmtp) cc_final: 0.7083 (mmmt) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.6904 time to fit residues: 111.4737 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 91 optimal weight: 0.0770 chunk 48 optimal weight: 0.3980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105871 restraints weight = 9354.389| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.56 r_work: 0.2953 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11176 Z= 0.104 Angle : 0.493 6.924 15193 Z= 0.252 Chirality : 0.039 0.149 1819 Planarity : 0.004 0.048 1916 Dihedral : 7.995 118.972 1628 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 16.33 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.22), residues: 1444 helix: 2.08 (0.17), residues: 892 sheet: -0.57 (0.52), residues: 87 loop : 0.02 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.022 0.001 TYR A 381 PHE 0.009 0.001 PHE A 109 TRP 0.012 0.001 TRP B 71 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00206 (11175) covalent geometry : angle 0.49300 (15191) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.32123 ( 2) hydrogen bonds : bond 0.04246 ( 691) hydrogen bonds : angle 4.20624 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6330.27 seconds wall clock time: 108 minutes 7.85 seconds (6487.85 seconds total)