Starting phenix.real_space_refine on Sat Jul 20 16:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/07_2024/7zrh_14914.cif" } resolution = 3.4 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= 0.007 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: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7123 2.51 5 N 1822 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11014 Number of models: 1 Model: "" Number of chains: 6 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: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {' K': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' K': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.92, per 1000 atoms: 0.63 Number of scatterers: 11014 At special positions: 0 Unit cell: (89.056, 115.368, 144.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 7 19.00 S 62 16.00 P 5 15.00 O 1995 8.00 N 1822 7.00 C 7123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 62.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.802A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.756A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.103A 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 98 through 111 removed outlier: 3.625A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.694A 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 removed outlier: 3.639A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.923A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.388A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.730A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.423A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.473A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.573A 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 399 removed outlier: 4.172A pdb=" N LEU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 436 removed outlier: 4.562A 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 443 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 523 through 542 removed outlier: 4.282A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.554A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.729A 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 168 through 172 removed outlier: 3.519A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.981A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 98 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.632A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.957A 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 284 removed outlier: 5.892A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.650A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.822A pdb=" N LEU B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.674A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.875A 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 529 removed outlier: 3.636A pdb=" N GLN B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.660A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix removed outlier: 3.616A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 3.888A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.099A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix 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 'C' and resid 42 through 44 removed outlier: 6.073A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.576A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.665A pdb=" N VAL B 121 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 133 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 189 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.605A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N MET B 535 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY B 517 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 516 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 306 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 470 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA9, first strand: chain 'B' and resid 373 through 374 removed outlier: 4.104A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1935 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: 3.19 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1856 1.32 - 1.45: 2658 1.45 - 1.57: 6567 1.57 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11205 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.74e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OB3 CDL B 801 " pdb=" PB2 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.19e+00 bond pdb=" OA3 CDL B 801 " pdb=" PA1 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.17e+00 bond pdb=" C51 CDL A 607 " pdb=" C52 CDL A 607 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.58e+00 ... (remaining 11200 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.92: 289 105.92 - 112.99: 6109 112.99 - 120.05: 3935 120.05 - 127.12: 4752 127.12 - 134.19: 119 Bond angle restraints: 15204 Sorted by residual: angle pdb=" CB LYS B 419 " pdb=" CG LYS B 419 " pdb=" CD LYS B 419 " ideal model delta sigma weight residual 111.30 120.03 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS B 102 " pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL A 376 " pdb=" CA VAL A 376 " pdb=" CB VAL A 376 " ideal model delta sigma weight residual 111.23 114.94 -3.71 1.01e+00 9.80e-01 1.35e+01 angle pdb=" N GLY B 452 " pdb=" CA GLY B 452 " pdb=" C GLY B 452 " ideal model delta sigma weight residual 110.95 116.91 -5.96 1.70e+00 3.46e-01 1.23e+01 angle pdb=" N GLY A 375 " pdb=" CA GLY A 375 " pdb=" C GLY A 375 " ideal model delta sigma weight residual 111.78 117.31 -5.53 1.69e+00 3.50e-01 1.07e+01 ... (remaining 15199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5949 17.95 - 35.90: 601 35.90 - 53.85: 139 53.85 - 71.80: 35 71.80 - 89.75: 11 Dihedral angle restraints: 6735 sinusoidal: 2629 harmonic: 4106 Sorted by residual: dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+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 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta harmonic sigma weight residual 180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1232 0.042 - 0.084: 427 0.084 - 0.126: 126 0.126 - 0.167: 21 0.167 - 0.209: 5 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 313 " pdb=" CA THR B 313 " pdb=" OG1 THR B 313 " pdb=" CG2 THR B 313 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA4 CDL B 801 " pdb=" CA3 CDL B 801 " pdb=" CA6 CDL B 801 " pdb=" OA6 CDL B 801 " both_signs ideal model delta sigma weight residual False -2.57 -2.38 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 1808 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 121 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 122 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 262 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO A 263 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 75 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3200 2.82 - 3.40: 12416 3.40 - 3.98: 21354 3.98 - 4.56: 30546 4.56 - 5.14: 44405 Nonbonded interactions: 111921 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP B 329 " pdb=" OG1 THR B 332 " model vdw 2.267 2.440 nonbonded pdb=" O GLN B 318 " pdb=" OG SER B 351 " model vdw 2.274 2.440 nonbonded pdb=" O LEU B 239 " pdb=" OG SER B 243 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR B 471 " pdb=" OD1 ASP B 473 " model vdw 2.298 2.440 ... (remaining 111916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.730 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.430 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11205 Z= 0.264 Angle : 0.748 8.731 15204 Z= 0.386 Chirality : 0.047 0.209 1811 Planarity : 0.006 0.065 1909 Dihedral : 15.889 89.752 4097 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.07 (0.20), residues: 1439 helix: 0.20 (0.16), residues: 843 sheet: -1.36 (0.74), residues: 56 loop : -2.07 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 655 HIS 0.003 0.001 HIS A 451 PHE 0.029 0.002 PHE A 260 TYR 0.023 0.002 TYR C 170 ARG 0.012 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.097 Fit side-chains REVERT: A 71 MET cc_start: 0.8244 (mmt) cc_final: 0.7738 (mmt) REVERT: A 130 MET cc_start: 0.8478 (ttp) cc_final: 0.8118 (ttm) REVERT: B 77 LEU cc_start: 0.7944 (tt) cc_final: 0.7736 (tt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2082 time to fit residues: 46.1716 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN C 154 GLN B 316 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11205 Z= 0.195 Angle : 0.517 7.350 15204 Z= 0.264 Chirality : 0.039 0.144 1811 Planarity : 0.004 0.052 1909 Dihedral : 11.311 59.973 1715 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.44 % Allowed : 7.05 % Favored : 92.51 % 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: -0.25 (0.21), residues: 1439 helix: 0.95 (0.17), residues: 856 sheet: -1.04 (0.66), residues: 69 loop : -1.98 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 260 TYR 0.030 0.002 TYR A 381 ARG 0.005 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.232 Fit side-chains REVERT: A 130 MET cc_start: 0.8420 (ttp) cc_final: 0.7995 (ttm) REVERT: B 23 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6061 (mttt) outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.2141 time to fit residues: 39.9020 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN C 154 GLN B 16 GLN B 80 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11205 Z= 0.338 Angle : 0.591 7.441 15204 Z= 0.299 Chirality : 0.042 0.150 1811 Planarity : 0.004 0.051 1909 Dihedral : 10.667 59.921 1715 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.15 % Allowed : 10.31 % Favored : 88.55 % 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: -0.14 (0.21), residues: 1439 helix: 1.05 (0.17), residues: 844 sheet: -1.31 (0.63), residues: 74 loop : -1.82 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.005 0.001 HIS A 451 PHE 0.023 0.002 PHE A 354 TYR 0.028 0.002 TYR A 381 ARG 0.003 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.067 Fit side-chains REVERT: A 130 MET cc_start: 0.8403 (ttp) cc_final: 0.8150 (ttm) REVERT: A 445 MET cc_start: 0.8498 (mmt) cc_final: 0.7407 (mmt) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.2071 time to fit residues: 40.6581 Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 522 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 123 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN C 154 GLN B 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11205 Z= 0.170 Angle : 0.502 7.286 15204 Z= 0.256 Chirality : 0.039 0.139 1811 Planarity : 0.004 0.051 1909 Dihedral : 10.001 59.532 1715 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.23 % Allowed : 11.72 % Favored : 87.05 % 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: 0.18 (0.22), residues: 1439 helix: 1.33 (0.18), residues: 852 sheet: -1.55 (0.61), residues: 79 loop : -1.73 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 PHE 0.012 0.001 PHE A 260 TYR 0.023 0.001 TYR A 381 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.275 Fit side-chains REVERT: A 130 MET cc_start: 0.8447 (ttp) cc_final: 0.8184 (ttm) REVERT: A 413 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 445 MET cc_start: 0.8307 (mmt) cc_final: 0.7161 (mmt) REVERT: B 25 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7592 (pp) REVERT: B 383 MET cc_start: 0.5686 (ttp) cc_final: 0.5127 (tmm) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.1965 time to fit residues: 37.4122 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 255 GLN A 482 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11205 Z= 0.271 Angle : 0.541 7.330 15204 Z= 0.274 Chirality : 0.041 0.137 1811 Planarity : 0.004 0.052 1909 Dihedral : 9.697 58.236 1715 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.41 % Allowed : 12.78 % Favored : 85.81 % 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: 0.18 (0.22), residues: 1439 helix: 1.30 (0.17), residues: 847 sheet: -1.02 (0.67), residues: 69 loop : -1.73 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 354 TYR 0.024 0.001 TYR A 381 ARG 0.003 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.086 Fit side-chains REVERT: A 130 MET cc_start: 0.8463 (ttp) cc_final: 0.8258 (ttm) REVERT: A 413 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: B 25 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7646 (pp) REVERT: B 383 MET cc_start: 0.5844 (ttp) cc_final: 0.5290 (tmm) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.2024 time to fit residues: 37.6044 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11205 Z= 0.164 Angle : 0.497 7.247 15204 Z= 0.252 Chirality : 0.039 0.132 1811 Planarity : 0.003 0.050 1909 Dihedral : 9.139 59.135 1715 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 13.13 % Favored : 85.29 % 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: 0.38 (0.22), residues: 1439 helix: 1.50 (0.18), residues: 852 sheet: -1.48 (0.69), residues: 59 loop : -1.67 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.003 0.000 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.023 0.001 TYR A 381 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.209 Fit side-chains REVERT: A 227 MET cc_start: 0.8358 (mmp) cc_final: 0.7939 (mmp) REVERT: A 413 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 25 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 383 MET cc_start: 0.5801 (ttp) cc_final: 0.5242 (tmm) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.2122 time to fit residues: 40.5518 Evaluate side-chains 122 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN B 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11205 Z= 0.278 Angle : 0.543 7.298 15204 Z= 0.275 Chirality : 0.040 0.140 1811 Planarity : 0.004 0.050 1909 Dihedral : 9.208 59.173 1715 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % 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: 0.24 (0.22), residues: 1439 helix: 1.33 (0.18), residues: 848 sheet: -1.04 (0.66), residues: 75 loop : -1.69 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS A 451 PHE 0.011 0.001 PHE A 373 TYR 0.023 0.002 TYR A 381 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: A 520 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7789 (pt) REVERT: B 25 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7637 (pp) REVERT: B 383 MET cc_start: 0.5655 (ttp) cc_final: 0.5133 (tmm) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 0.2063 time to fit residues: 38.8141 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11205 Z= 0.162 Angle : 0.499 7.221 15204 Z= 0.253 Chirality : 0.039 0.131 1811 Planarity : 0.004 0.051 1909 Dihedral : 8.906 59.827 1715 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 14.45 % Favored : 83.96 % 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: 0.43 (0.22), residues: 1439 helix: 1.53 (0.18), residues: 848 sheet: -1.44 (0.70), residues: 59 loop : -1.60 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.011 0.001 PHE A 527 TYR 0.022 0.001 TYR A 381 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8357 (mmp) cc_final: 0.7947 (mmp) REVERT: A 413 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: B 25 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7673 (pp) REVERT: B 383 MET cc_start: 0.5592 (ttp) cc_final: 0.5068 (tmm) REVERT: B 535 MET cc_start: 0.7563 (mmm) cc_final: 0.7351 (mtp) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 0.1986 time to fit residues: 36.8379 Evaluate side-chains 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11205 Z= 0.223 Angle : 0.524 7.263 15204 Z= 0.265 Chirality : 0.040 0.197 1811 Planarity : 0.004 0.052 1909 Dihedral : 8.834 59.521 1715 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.50 % Allowed : 14.89 % Favored : 83.61 % 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: 0.41 (0.22), residues: 1439 helix: 1.48 (0.18), residues: 850 sheet: -1.01 (0.65), residues: 75 loop : -1.63 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.022 0.001 TYR A 381 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8417 (mmp) cc_final: 0.7993 (mmp) REVERT: A 413 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: B 25 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7670 (pp) REVERT: B 383 MET cc_start: 0.5666 (ttp) cc_final: 0.5143 (tmm) REVERT: B 535 MET cc_start: 0.7634 (mmm) cc_final: 0.7313 (mtp) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.2019 time to fit residues: 37.3996 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 11 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11205 Z= 0.157 Angle : 0.508 9.389 15204 Z= 0.256 Chirality : 0.039 0.260 1811 Planarity : 0.003 0.053 1909 Dihedral : 8.527 59.377 1715 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.32 % Allowed : 14.98 % Favored : 83.70 % 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: 0.52 (0.22), residues: 1439 helix: 1.61 (0.18), residues: 849 sheet: -1.41 (0.65), residues: 65 loop : -1.59 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.005 0.000 HIS A 451 PHE 0.011 0.001 PHE A 527 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: B 25 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 383 MET cc_start: 0.5642 (ttp) cc_final: 0.5130 (tmm) REVERT: B 535 MET cc_start: 0.7632 (mmm) cc_final: 0.7260 (mtp) outliers start: 15 outliers final: 13 residues processed: 124 average time/residue: 0.2135 time to fit residues: 39.7380 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108005 restraints weight = 14470.749| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.13 r_work: 0.2980 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11205 Z= 0.194 Angle : 0.535 10.919 15204 Z= 0.265 Chirality : 0.040 0.214 1811 Planarity : 0.004 0.053 1909 Dihedral : 8.440 58.144 1715 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.76 % Allowed : 14.54 % Favored : 83.70 % 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: 0.53 (0.22), residues: 1439 helix: 1.62 (0.18), residues: 846 sheet: -1.01 (0.64), residues: 75 loop : -1.62 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 PHE 0.011 0.001 PHE B 81 TYR 0.023 0.001 TYR A 381 ARG 0.002 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.98 seconds wall clock time: 39 minutes 33.10 seconds (2373.10 seconds total)