Starting phenix.real_space_refine on Mon Jun 9 23:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc4_70308/06_2025/9oc4_70308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc4_70308/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9oc4_70308/06_2025/9oc4_70308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc4_70308/06_2025/9oc4_70308.map" model { file = "/net/cci-nas-00/data/ceres_data/9oc4_70308/06_2025/9oc4_70308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc4_70308/06_2025/9oc4_70308.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.47, per 1000 atoms: 0.67 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.26 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: 3.86 Time building geometry restraints manager: 3.48 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.190 ------------------------------------------------------------------------------- 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 : 5.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS B 411 PHE 0.006 0.001 PHE B 242 TYR 0.018 0.001 TYR A 381 ARG 0.006 0.000 ARG B 3 Details of bonding type rmsd hydrogen bonds : bond 0.21901 ( 691) hydrogen bonds : angle 7.01162 ( 1998) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.14080 ( 2) covalent geometry : bond 0.00312 (11175) covalent geometry : angle 0.55584 (15191) *********************** 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 : 1.174 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: 1.4323 time to fit residues: 252.0179 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 : 1.241 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.160465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101543 restraints weight = 9096.627| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.64 r_work: 0.2973 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11176 Z= 0.193 Angle : 0.630 7.331 15193 Z= 0.330 Chirality : 0.045 0.167 1819 Planarity : 0.005 0.044 1916 Dihedral : 8.950 103.431 1631 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 2.55 % Allowed : 13.35 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1444 helix: 1.49 (0.17), residues: 875 sheet: -0.06 (0.54), residues: 81 loop : 0.09 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 71 HIS 0.004 0.001 HIS A 85 PHE 0.020 0.002 PHE A 527 TYR 0.022 0.003 TYR A 381 ARG 0.004 0.001 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.06904 ( 691) hydrogen bonds : angle 4.93229 ( 1998) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.42640 ( 2) covalent geometry : bond 0.00418 (11175) covalent geometry : angle 0.63033 (15191) *********************** 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 184 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.132 Fit side-chains REVERT: A 304 GLN cc_start: 0.8714 (mm110) cc_final: 0.8465 (mm-40) REVERT: A 306 ASN cc_start: 0.9030 (t0) cc_final: 0.8712 (t0) REVERT: B 107 ARG cc_start: 0.5644 (mtt180) cc_final: 0.5259 (mtt180) REVERT: B 145 GLU cc_start: 0.6818 (mp0) cc_final: 0.6576 (mm-30) REVERT: B 148 GLU cc_start: 0.7430 (tt0) cc_final: 0.5985 (tm-30) REVERT: B 175 SER cc_start: 0.7638 (m) cc_final: 0.7402 (t) REVERT: B 202 ARG cc_start: 0.6832 (ttt180) cc_final: 0.6498 (ttp80) REVERT: B 316 ASN cc_start: 0.7156 (t0) cc_final: 0.6945 (t0) REVERT: B 338 GLN cc_start: 0.6140 (mt0) cc_final: 0.5909 (mt0) REVERT: B 361 ASN cc_start: 0.6574 (OUTLIER) cc_final: 0.6081 (m-40) REVERT: B 383 MET cc_start: 0.7489 (ptm) cc_final: 0.6980 (ptm) REVERT: B 392 MET cc_start: 0.4167 (ttp) cc_final: 0.3307 (tpt) REVERT: B 446 LYS cc_start: 0.7250 (mmtp) cc_final: 0.6943 (mmmt) outliers start: 29 outliers final: 12 residues processed: 173 average time/residue: 1.3996 time to fit residues: 260.1103 Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.161219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102461 restraints weight = 9255.883| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.84 r_work: 0.2865 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1517 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= 0.149 Angle : 0.565 6.845 15193 Z= 0.294 Chirality : 0.042 0.163 1819 Planarity : 0.004 0.044 1916 Dihedral : 8.826 109.734 1628 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.55 % Allowed : 14.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.22), residues: 1444 helix: 1.75 (0.17), residues: 857 sheet: -0.25 (0.52), residues: 81 loop : -0.01 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.015 0.002 PHE A 527 TYR 0.023 0.002 TYR A 381 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 691) hydrogen bonds : angle 4.67653 ( 1998) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.45956 ( 2) covalent geometry : bond 0.00310 (11175) covalent geometry : angle 0.56464 (15191) *********************** 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 180 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 304 GLN cc_start: 0.8742 (mm110) cc_final: 0.8489 (mm-40) REVERT: A 306 ASN cc_start: 0.9097 (t0) cc_final: 0.8872 (t0) REVERT: A 389 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 107 ARG cc_start: 0.5650 (mtt180) cc_final: 0.5201 (mtt180) REVERT: B 110 ARG cc_start: 0.4645 (OUTLIER) cc_final: 0.4400 (mtt-85) REVERT: B 145 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6556 (mm-30) REVERT: B 148 GLU cc_start: 0.7341 (tt0) cc_final: 0.6004 (tm-30) REVERT: B 175 SER cc_start: 0.7624 (m) cc_final: 0.7355 (t) REVERT: B 202 ARG cc_start: 0.6789 (ttt180) cc_final: 0.6460 (ttp80) REVERT: B 316 ASN cc_start: 0.7223 (t0) cc_final: 0.7017 (t0) REVERT: B 338 GLN cc_start: 0.6074 (mt0) cc_final: 0.5846 (mt0) REVERT: B 361 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6142 (m-40) REVERT: B 383 MET cc_start: 0.7492 (ptm) cc_final: 0.6992 (ptm) REVERT: B 392 MET cc_start: 0.4280 (ttp) cc_final: 0.3285 (tpt) REVERT: B 446 LYS cc_start: 0.7267 (mmtp) cc_final: 0.6982 (mmmt) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 1.4252 time to fit residues: 258.1488 Evaluate side-chains 169 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 177 THR 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 B residue 678 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 126 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 154 GLN C 157 GLN C 165 GLN C 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104604 restraints weight = 9168.176| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.81 r_work: 0.2904 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1627 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= 0.121 Angle : 0.519 6.467 15193 Z= 0.268 Chirality : 0.040 0.157 1819 Planarity : 0.004 0.043 1916 Dihedral : 8.516 109.988 1628 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1444 helix: 1.88 (0.17), residues: 874 sheet: -0.36 (0.53), residues: 81 loop : -0.04 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.011 0.001 PHE A 527 TYR 0.022 0.002 TYR A 381 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 691) hydrogen bonds : angle 4.44964 ( 1998) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.39464 ( 2) covalent geometry : bond 0.00242 (11175) covalent geometry : angle 0.51876 (15191) *********************** 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 174 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8502 (mtt-85) cc_final: 0.8297 (ttt180) REVERT: A 205 ASN cc_start: 0.8560 (m-40) cc_final: 0.7840 (t0) REVERT: A 304 GLN cc_start: 0.8677 (mm110) cc_final: 0.8392 (mm-40) REVERT: A 306 ASN cc_start: 0.9060 (t0) cc_final: 0.8813 (t0) REVERT: A 389 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8637 (mp) REVERT: B 107 ARG cc_start: 0.5780 (mtt180) cc_final: 0.5294 (mtt180) REVERT: B 110 ARG cc_start: 0.4533 (OUTLIER) cc_final: 0.4195 (mtt-85) REVERT: B 145 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: B 148 GLU cc_start: 0.7366 (tt0) cc_final: 0.6054 (tm-30) REVERT: B 175 SER cc_start: 0.7594 (m) cc_final: 0.7299 (t) REVERT: B 202 ARG cc_start: 0.6684 (ttt180) cc_final: 0.6458 (ttp80) REVERT: B 213 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6279 (mpp-170) REVERT: B 383 MET cc_start: 0.7499 (ptm) cc_final: 0.6974 (ptm) REVERT: B 392 MET cc_start: 0.4466 (ttp) cc_final: 0.3409 (tpt) REVERT: B 446 LYS cc_start: 0.7297 (mmtp) cc_final: 0.7040 (mmmt) outliers start: 27 outliers final: 15 residues processed: 165 average time/residue: 1.4878 time to fit residues: 262.4193 Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 147 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101064 restraints weight = 9161.319| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.72 r_work: 0.2930 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11176 Z= 0.187 Angle : 0.610 7.292 15193 Z= 0.317 Chirality : 0.044 0.170 1819 Planarity : 0.005 0.049 1916 Dihedral : 8.948 117.884 1628 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.81 % Allowed : 14.40 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1444 helix: 1.68 (0.17), residues: 862 sheet: -0.46 (0.50), residues: 91 loop : 0.00 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 71 HIS 0.004 0.001 HIS B 563 PHE 0.021 0.002 PHE A 527 TYR 0.022 0.003 TYR A 381 ARG 0.004 0.001 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.06177 ( 691) hydrogen bonds : angle 4.68256 ( 1998) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.59763 ( 2) covalent geometry : bond 0.00409 (11175) covalent geometry : angle 0.61023 (15191) *********************** 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 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 52 VAL cc_start: 0.7884 (t) cc_final: 0.7555 (m) REVERT: A 304 GLN cc_start: 0.8786 (mm110) cc_final: 0.8541 (mm-40) REVERT: A 306 ASN cc_start: 0.9157 (t0) cc_final: 0.8932 (t0) REVERT: A 389 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 414 MET cc_start: 0.8696 (mmp) cc_final: 0.8480 (mmm) REVERT: B 110 ARG cc_start: 0.4558 (OUTLIER) cc_final: 0.4245 (mtt-85) REVERT: B 145 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: B 148 GLU cc_start: 0.7343 (tt0) cc_final: 0.6109 (tm-30) REVERT: B 175 SER cc_start: 0.7562 (m) cc_final: 0.7147 (m) REVERT: B 202 ARG cc_start: 0.6832 (ttt180) cc_final: 0.6507 (ttp80) REVERT: B 213 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6373 (mpp-170) REVERT: B 383 MET cc_start: 0.7489 (ptm) cc_final: 0.7003 (ptm) REVERT: B 392 MET cc_start: 0.4569 (ttp) cc_final: 0.3450 (tpt) REVERT: B 446 LYS cc_start: 0.7273 (mmtp) cc_final: 0.7030 (mmmt) outliers start: 32 outliers final: 20 residues processed: 168 average time/residue: 1.5475 time to fit residues: 278.9077 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 : 1.256 ------------------------------------------------------------------------------- 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 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 131 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.161558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103330 restraints weight = 9196.826| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.77 r_work: 0.2883 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1757 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 : 0.535 6.762 15193 Z= 0.278 Chirality : 0.040 0.161 1819 Planarity : 0.004 0.051 1916 Dihedral : 8.690 119.386 1628 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 15.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1444 helix: 1.82 (0.17), residues: 869 sheet: -0.62 (0.50), residues: 92 loop : -0.10 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.013 0.001 PHE A 527 TYR 0.023 0.002 TYR A 381 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 691) hydrogen bonds : angle 4.48552 ( 1998) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.45551 ( 2) covalent geometry : bond 0.00267 (11175) covalent geometry : angle 0.53509 (15191) *********************** 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 166 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8354 (ttt-90) REVERT: A 205 ASN cc_start: 0.8616 (m-40) cc_final: 0.7869 (t0) REVERT: A 304 GLN cc_start: 0.8721 (mm110) cc_final: 0.8451 (mm-40) REVERT: A 306 ASN cc_start: 0.9108 (t0) cc_final: 0.8850 (t0) REVERT: A 389 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 414 MET cc_start: 0.8677 (mmp) cc_final: 0.8466 (mmm) REVERT: B 110 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.4213 (mtt-85) REVERT: B 145 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: B 148 GLU cc_start: 0.7388 (tt0) cc_final: 0.6148 (tm-30) REVERT: B 175 SER cc_start: 0.7558 (m) cc_final: 0.7300 (t) REVERT: B 202 ARG cc_start: 0.6773 (ttt180) cc_final: 0.6489 (ttp80) REVERT: B 213 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6291 (mpp-170) REVERT: B 383 MET cc_start: 0.7510 (ptm) cc_final: 0.7081 (ptm) REVERT: B 392 MET cc_start: 0.4599 (ttp) cc_final: 0.3436 (tpt) REVERT: B 446 LYS cc_start: 0.7325 (mmtp) cc_final: 0.6988 (mmmt) REVERT: C 135 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8331 (pm20) outliers start: 25 outliers final: 15 residues processed: 159 average time/residue: 1.4288 time to fit residues: 243.1856 Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 73 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 79 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 173 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 = 0.162756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104393 restraints weight = 9282.804| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.75 r_work: 0.3023 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1769 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= 0.117 Angle : 0.515 6.557 15193 Z= 0.266 Chirality : 0.039 0.156 1819 Planarity : 0.004 0.053 1916 Dihedral : 8.453 117.792 1628 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.28 % Allowed : 14.93 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.22), residues: 1444 helix: 1.96 (0.17), residues: 877 sheet: -0.57 (0.52), residues: 87 loop : -0.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.001 0.001 HIS A 523 PHE 0.011 0.001 PHE A 109 TYR 0.023 0.001 TYR A 381 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 691) hydrogen bonds : angle 4.37080 ( 1998) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.40699 ( 2) covalent geometry : bond 0.00232 (11175) covalent geometry : angle 0.51532 (15191) *********************** 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 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8321 (ttt180) REVERT: A 205 ASN cc_start: 0.8655 (m-40) cc_final: 0.7922 (t0) REVERT: A 304 GLN cc_start: 0.8728 (mm110) cc_final: 0.8451 (mm-40) REVERT: A 306 ASN cc_start: 0.9089 (t0) cc_final: 0.8766 (t0) REVERT: A 389 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 414 MET cc_start: 0.8708 (mmp) cc_final: 0.8490 (mmm) REVERT: B 110 ARG cc_start: 0.4534 (OUTLIER) cc_final: 0.3952 (mpt90) REVERT: B 145 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: B 148 GLU cc_start: 0.7431 (tt0) cc_final: 0.6068 (tm-30) REVERT: B 175 SER cc_start: 0.7497 (m) cc_final: 0.7246 (t) REVERT: B 213 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6256 (mpp-170) REVERT: B 383 MET cc_start: 0.7478 (ptm) cc_final: 0.6970 (ptm) REVERT: B 392 MET cc_start: 0.4543 (ttp) cc_final: 0.3374 (tpt) REVERT: B 446 LYS cc_start: 0.7293 (mmtp) cc_final: 0.6971 (mmmt) REVERT: B 497 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: C 135 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (pm20) outliers start: 26 outliers final: 15 residues processed: 156 average time/residue: 1.5860 time to fit residues: 265.7177 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 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 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 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103628 restraints weight = 9228.515| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.60 r_work: 0.2993 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1788 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= 0.121 Angle : 0.520 6.632 15193 Z= 0.269 Chirality : 0.040 0.156 1819 Planarity : 0.004 0.055 1916 Dihedral : 8.370 116.227 1628 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.11 % Allowed : 15.19 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1444 helix: 1.98 (0.17), residues: 877 sheet: -0.59 (0.52), residues: 87 loop : -0.08 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 71 HIS 0.002 0.001 HIS B 611 PHE 0.012 0.001 PHE A 527 TYR 0.022 0.001 TYR A 381 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 691) hydrogen bonds : angle 4.37093 ( 1998) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.38098 ( 2) covalent geometry : bond 0.00244 (11175) covalent geometry : angle 0.52036 (15191) *********************** 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 160 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8307 (ttt180) REVERT: A 205 ASN cc_start: 0.8645 (m-40) cc_final: 0.7900 (t0) REVERT: A 304 GLN cc_start: 0.8719 (mm110) cc_final: 0.8439 (mm-40) REVERT: A 306 ASN cc_start: 0.9087 (t0) cc_final: 0.8765 (t0) REVERT: A 389 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 110 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.3959 (mpt90) REVERT: B 145 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: B 148 GLU cc_start: 0.7480 (tt0) cc_final: 0.6098 (tm-30) REVERT: B 175 SER cc_start: 0.7493 (m) cc_final: 0.7095 (m) REVERT: B 213 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6229 (mpp-170) REVERT: B 383 MET cc_start: 0.7470 (ptm) cc_final: 0.6950 (ptm) REVERT: B 392 MET cc_start: 0.4537 (ttp) cc_final: 0.3362 (tpt) REVERT: B 446 LYS cc_start: 0.7292 (mmtp) cc_final: 0.6978 (mmmt) REVERT: B 497 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: C 135 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8299 (pm20) outliers start: 24 outliers final: 15 residues processed: 153 average time/residue: 1.4554 time to fit residues: 238.6233 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 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 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 94 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103100 restraints weight = 9247.720| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.75 r_work: 0.2979 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1819 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= 0.136 Angle : 0.543 6.882 15193 Z= 0.281 Chirality : 0.041 0.159 1819 Planarity : 0.004 0.056 1916 Dihedral : 8.434 116.565 1628 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.46 % Allowed : 14.93 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1444 helix: 1.97 (0.17), residues: 870 sheet: -0.58 (0.52), residues: 87 loop : -0.12 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.015 0.001 PHE A 527 TYR 0.023 0.002 TYR A 381 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 691) hydrogen bonds : angle 4.43922 ( 1998) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.40794 ( 2) covalent geometry : bond 0.00283 (11175) covalent geometry : angle 0.54336 (15191) *********************** 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: 28 poor density : 139 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8652 (m-40) cc_final: 0.7932 (t0) REVERT: A 304 GLN cc_start: 0.8760 (mm110) cc_final: 0.8485 (mm-40) REVERT: A 306 ASN cc_start: 0.9119 (t0) cc_final: 0.8845 (t0) REVERT: A 389 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8680 (mp) REVERT: B 110 ARG cc_start: 0.4547 (OUTLIER) cc_final: 0.3974 (mpt90) REVERT: B 145 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: B 148 GLU cc_start: 0.7455 (tt0) cc_final: 0.6069 (tm-30) REVERT: B 175 SER cc_start: 0.7519 (m) cc_final: 0.7131 (m) REVERT: B 213 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6293 (mpp-170) REVERT: B 383 MET cc_start: 0.7476 (ptm) cc_final: 0.6970 (ptm) REVERT: B 392 MET cc_start: 0.4576 (ttp) cc_final: 0.3439 (tpt) REVERT: B 446 LYS cc_start: 0.7296 (mmtp) cc_final: 0.7058 (mmmt) REVERT: C 135 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8372 (pm20) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 1.4752 time to fit residues: 252.1066 Evaluate side-chains 160 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 89 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.162067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103394 restraints weight = 9205.371| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.71 r_work: 0.2989 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1829 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= 0.132 Angle : 0.539 6.899 15193 Z= 0.278 Chirality : 0.040 0.158 1819 Planarity : 0.004 0.056 1916 Dihedral : 8.395 116.542 1628 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 15.19 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1444 helix: 1.95 (0.17), residues: 876 sheet: -0.59 (0.52), residues: 87 loop : -0.12 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.014 0.001 PHE A 527 TYR 0.022 0.002 TYR A 381 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 691) hydrogen bonds : angle 4.41901 ( 1998) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.41730 ( 2) covalent geometry : bond 0.00272 (11175) covalent geometry : angle 0.53891 (15191) ********************** 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 165 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8650 (m-40) cc_final: 0.7940 (t0) REVERT: A 304 GLN cc_start: 0.8756 (mm110) cc_final: 0.8483 (mm-40) REVERT: A 306 ASN cc_start: 0.9111 (t0) cc_final: 0.8836 (t0) REVERT: A 389 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 110 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.4004 (mpt90) REVERT: B 145 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: B 148 GLU cc_start: 0.7479 (tt0) cc_final: 0.6109 (tm-30) REVERT: B 175 SER cc_start: 0.7507 (m) cc_final: 0.7127 (m) REVERT: B 213 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6294 (mpp-170) REVERT: B 383 MET cc_start: 0.7477 (ptm) cc_final: 0.6969 (ptm) REVERT: B 392 MET cc_start: 0.4546 (ttp) cc_final: 0.3379 (tpt) REVERT: B 446 LYS cc_start: 0.7332 (mmtp) cc_final: 0.7083 (mmmt) REVERT: C 135 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8316 (pm20) outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 1.4381 time to fit residues: 243.6024 Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 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 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 40 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 154 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 = 0.3882 r_free = 0.3882 target = 0.162889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103861 restraints weight = 9206.570| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.53 r_work: 0.2912 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1856 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= 0.119 Angle : 0.520 6.785 15193 Z= 0.268 Chirality : 0.040 0.156 1819 Planarity : 0.004 0.056 1916 Dihedral : 8.237 114.927 1628 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.84 % Allowed : 15.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1444 helix: 2.02 (0.17), residues: 877 sheet: -0.51 (0.52), residues: 86 loop : -0.10 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.011 0.001 PHE A 527 TYR 0.022 0.001 TYR A 381 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 691) hydrogen bonds : angle 4.35220 ( 1998) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.37291 ( 2) covalent geometry : bond 0.00238 (11175) covalent geometry : angle 0.51988 (15191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13480.80 seconds wall clock time: 231 minutes 23.27 seconds (13883.27 seconds total)