Starting phenix.real_space_refine on Mon Dec 30 05:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.map" model { file = "/net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zri_14915/12_2024/7zri_14915.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1040 atoms to isotropic. 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. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Unusual residues: {' K': 5, 'CDL': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {' K': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.69, per 1000 atoms: 0.61 Number of scatterers: 11014 At special positions: 0 Unit cell: (104.236, 110.308, 155.848, 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 - 3.00 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 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: 60 helices and 8 sheets defined 62.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 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 51 removed outlier: 3.586A 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 Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.584A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.788A 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 178 through 193 removed outlier: 4.149A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.027A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.527A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 305 removed outlier: 4.078A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.432A 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: 3.737A 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 379 through 399 removed outlier: 3.718A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 435 removed outlier: 3.754A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.726A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.286A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 524 through 540 Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.954A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 20 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 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 177 through 190 Processing helix chain 'D' and resid 5 through 25 removed outlier: 3.903A pdb=" N LEU D 10 " --> pdb=" O ILE D 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.906A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 98 removed outlier: 3.563A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 237 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.972A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.838A 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 269 Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.887A 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 361 Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.221A pdb=" N HIS B 371 " --> pdb=" O GLN B 368 " (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 453 through 464 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.673A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.725A pdb=" N GLY B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 556 through 582 removed outlier: 4.205A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 4.098A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.685A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 removed outlier: 4.013A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN B 606 " --> pdb=" O ASN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.008A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.073A 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 648 through 679 removed outlier: 4.370A 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 45 removed outlier: 6.086A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.789A pdb=" N VAL C 175 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 140 removed outlier: 3.522A pdb=" N ASP B 138 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR B 180 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.006A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 306 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 323 removed outlier: 7.735A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 393 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 378 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY B 385 " --> pdb=" O PRO B 376 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1923 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: 3.87 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1774 1.31 - 1.43: 2711 1.43 - 1.56: 6596 1.56 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11205 Sorted by residual: bond pdb=" CB7 CDL B 702 " pdb=" OB8 CDL B 702 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.49e+01 bond pdb=" CB7 CDL A 606 " pdb=" OB8 CDL A 606 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.32e+01 bond pdb=" CA7 CDL A 606 " pdb=" OA8 CDL A 606 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.21e+01 bond pdb=" CA7 CDL B 702 " pdb=" OA8 CDL B 702 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.10e-02 8.26e+03 5.66e+01 bond pdb=" OB2 CDL A 606 " pdb=" PB2 CDL A 606 " ideal model delta sigma weight residual 1.579 1.668 -0.089 1.50e-02 4.44e+03 3.49e+01 ... (remaining 11200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 14582 1.96 - 3.92: 408 3.92 - 5.88: 168 5.88 - 7.84: 32 7.84 - 9.80: 14 Bond angle restraints: 15204 Sorted by residual: angle pdb=" C11 CDL B 702 " pdb=" CA5 CDL B 702 " pdb=" OA6 CDL B 702 " ideal model delta sigma weight residual 111.33 121.01 -9.68 1.32e+00 5.72e-01 5.36e+01 angle pdb=" C51 CDL B 702 " pdb=" CB5 CDL B 702 " pdb=" OB6 CDL B 702 " ideal model delta sigma weight residual 111.33 120.39 -9.06 1.32e+00 5.72e-01 4.69e+01 angle pdb=" C11 CDL A 606 " pdb=" CA5 CDL A 606 " pdb=" OA6 CDL A 606 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 angle pdb=" C51 CDL A 606 " pdb=" CB5 CDL A 606 " pdb=" OB6 CDL A 606 " ideal model delta sigma weight residual 111.33 119.99 -8.66 1.32e+00 5.72e-01 4.29e+01 angle pdb=" C31 CDL A 606 " pdb=" CA7 CDL A 606 " pdb=" OA8 CDL A 606 " ideal model delta sigma weight residual 111.64 121.44 -9.80 1.65e+00 3.69e-01 3.54e+01 ... (remaining 15199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5834 16.81 - 33.63: 661 33.63 - 50.44: 170 50.44 - 67.25: 58 67.25 - 84.06: 12 Dihedral angle restraints: 6735 sinusoidal: 2629 harmonic: 4106 Sorted by residual: 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 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA THR B 236 " pdb=" C THR B 236 " pdb=" N ALA B 237 " pdb=" CA ALA B 237 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ALA B 106 " pdb=" C ALA B 106 " pdb=" N ARG B 107 " pdb=" CA ARG B 107 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1231 0.042 - 0.084: 418 0.084 - 0.127: 143 0.127 - 0.169: 14 0.169 - 0.211: 5 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CB THR B 516 " pdb=" CA THR B 516 " pdb=" OG1 THR B 516 " pdb=" CG2 THR B 516 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 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 ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1808 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO B 216 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 586 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS B 586 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS B 586 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 587 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 126 " 0.009 2.00e-02 2.50e+03 1.59e-02 5.07e+00 pdb=" CG TYR A 126 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 126 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 126 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 126 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 126 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 126 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.78: 2429 2.78 - 3.37: 12346 3.37 - 3.96: 21390 3.96 - 4.55: 29872 4.55 - 5.14: 44616 Nonbonded interactions: 110653 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.228 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.274 3.040 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 251 " model vdw 2.287 3.040 nonbonded pdb=" O LEU C 14 " pdb=" OG1 THR C 18 " model vdw 2.302 3.040 ... (remaining 110648 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 group one per residue 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.006 0.089 11205 Z= 0.386 Angle : 0.919 9.799 15204 Z= 0.465 Chirality : 0.047 0.211 1811 Planarity : 0.006 0.064 1909 Dihedral : 16.165 84.064 4097 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.22 (0.21), residues: 1439 helix: -0.00 (0.17), residues: 857 sheet: -1.69 (0.59), residues: 77 loop : -1.98 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 32 HIS 0.002 0.000 HIS A 242 PHE 0.029 0.002 PHE A 260 TYR 0.033 0.002 TYR A 126 ARG 0.005 0.000 ARG A 172 *********************** 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 144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.209 Fit side-chains REVERT: A 363 MET cc_start: 0.9147 (ttm) cc_final: 0.8814 (ttp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2037 time to fit residues: 44.3065 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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: 8.9990 chunk 108 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN C 165 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11205 Z= 0.349 Angle : 0.620 6.362 15204 Z= 0.317 Chirality : 0.042 0.226 1811 Planarity : 0.004 0.055 1909 Dihedral : 11.492 74.721 1715 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.88 % Allowed : 9.52 % Favored : 89.60 % 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: -0.55 (0.22), residues: 1439 helix: 0.64 (0.18), residues: 869 sheet: -1.68 (0.54), residues: 87 loop : -1.92 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.005 0.001 HIS A 242 PHE 0.016 0.002 PHE A 354 TYR 0.025 0.002 TYR A 381 ARG 0.003 0.000 ARG B 89 *********************** 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.168 Fit side-chains REVERT: A 176 TRP cc_start: 0.7223 (m-10) cc_final: 0.6940 (m-10) REVERT: B 469 MET cc_start: 0.7677 (tmm) cc_final: 0.7198 (ttt) outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.2106 time to fit residues: 41.5618 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 0.0010 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11205 Z= 0.290 Angle : 0.580 7.706 15204 Z= 0.293 Chirality : 0.041 0.233 1811 Planarity : 0.004 0.057 1909 Dihedral : 10.668 75.278 1715 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.06 % Allowed : 13.04 % Favored : 85.90 % 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 (0.22), residues: 1439 helix: 0.90 (0.18), residues: 872 sheet: -1.78 (0.53), residues: 87 loop : -1.82 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 373 TYR 0.023 0.002 TYR A 381 ARG 0.002 0.000 ARG B 89 *********************** 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.294 Fit side-chains REVERT: A 176 TRP cc_start: 0.7278 (m-10) cc_final: 0.6786 (m-10) REVERT: C 130 ASN cc_start: 0.8381 (t0) cc_final: 0.8062 (t0) REVERT: C 154 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7583 (tp-100) REVERT: B 469 MET cc_start: 0.7666 (tmm) cc_final: 0.7283 (ttt) outliers start: 12 outliers final: 11 residues processed: 132 average time/residue: 0.2037 time to fit residues: 41.1211 Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11205 Z= 0.163 Angle : 0.524 8.603 15204 Z= 0.263 Chirality : 0.039 0.213 1811 Planarity : 0.004 0.055 1909 Dihedral : 9.999 74.027 1715 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.23 % Allowed : 14.36 % Favored : 84.41 % 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: 0.12 (0.22), residues: 1439 helix: 1.21 (0.18), residues: 864 sheet: -1.76 (0.53), residues: 84 loop : -1.62 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.018 0.001 TYR A 381 ARG 0.002 0.000 ARG C 68 *********************** 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 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7281 (m-10) cc_final: 0.6796 (m-10) REVERT: C 130 ASN cc_start: 0.8341 (t0) cc_final: 0.8074 (t0) outliers start: 14 outliers final: 9 residues processed: 137 average time/residue: 0.2185 time to fit residues: 44.9808 Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR 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: 5.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11205 Z= 0.274 Angle : 0.562 8.657 15204 Z= 0.283 Chirality : 0.040 0.138 1811 Planarity : 0.004 0.055 1909 Dihedral : 9.757 75.703 1715 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.32 % Allowed : 16.56 % Favored : 82.11 % 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: 0.08 (0.22), residues: 1439 helix: 1.15 (0.18), residues: 874 sheet: -1.76 (0.54), residues: 84 loop : -1.62 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 PHE 0.012 0.001 PHE A 373 TYR 0.022 0.002 TYR A 381 ARG 0.002 0.000 ARG B 89 *********************** 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 ASN cc_start: 0.8372 (t0) cc_final: 0.8086 (t0) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.2166 time to fit residues: 42.5164 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR 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: 9.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 64 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11205 Z= 0.153 Angle : 0.510 8.940 15204 Z= 0.256 Chirality : 0.038 0.136 1811 Planarity : 0.004 0.056 1909 Dihedral : 9.308 74.431 1715 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.50 % Allowed : 16.83 % Favored : 81.67 % 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: 0.39 (0.23), residues: 1439 helix: 1.43 (0.18), residues: 859 sheet: -1.76 (0.54), residues: 84 loop : -1.48 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 186 HIS 0.001 0.000 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.017 0.001 TYR A 381 ARG 0.002 0.000 ARG B 504 *********************** 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 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6611 (ptt) REVERT: C 130 ASN cc_start: 0.8323 (t0) cc_final: 0.8084 (t0) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.2073 time to fit residues: 42.6586 Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11205 Z= 0.167 Angle : 0.520 9.179 15204 Z= 0.258 Chirality : 0.039 0.138 1811 Planarity : 0.003 0.055 1909 Dihedral : 9.000 74.691 1715 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.67 % Allowed : 17.53 % Favored : 80.79 % 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: 0.50 (0.23), residues: 1439 helix: 1.52 (0.18), residues: 858 sheet: -1.71 (0.55), residues: 84 loop : -1.43 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 PHE 0.010 0.001 PHE A 109 TYR 0.017 0.001 TYR A 381 ARG 0.001 0.000 ARG B 504 *********************** 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 148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 MET cc_start: 0.8654 (mmt) cc_final: 0.8438 (mmp) REVERT: A 446 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7985 (tt) REVERT: C 75 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6667 (ptt) REVERT: C 130 ASN cc_start: 0.8311 (t0) cc_final: 0.8090 (t0) REVERT: B 282 MET cc_start: 0.8699 (tpp) cc_final: 0.8391 (tpp) REVERT: B 392 MET cc_start: 0.2595 (mtm) cc_final: 0.1934 (ppp) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 0.2094 time to fit residues: 44.9652 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11205 Z= 0.168 Angle : 0.530 9.302 15204 Z= 0.264 Chirality : 0.039 0.135 1811 Planarity : 0.004 0.055 1909 Dihedral : 8.769 75.064 1715 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.94 % Allowed : 17.80 % Favored : 80.26 % 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: 0.58 (0.23), residues: 1439 helix: 1.56 (0.18), residues: 858 sheet: -1.58 (0.60), residues: 74 loop : -1.38 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.024 0.002 TYR A 126 ARG 0.001 0.000 ARG B 504 *********************** 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 147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: A 446 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7808 (tt) REVERT: C 75 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6684 (ptt) REVERT: C 130 ASN cc_start: 0.8271 (t0) cc_final: 0.8065 (t0) REVERT: B 109 LEU cc_start: 0.0641 (OUTLIER) cc_final: 0.0358 (pp) REVERT: B 282 MET cc_start: 0.8646 (tpp) cc_final: 0.8310 (tpp) REVERT: B 392 MET cc_start: 0.2475 (mtm) cc_final: 0.1880 (ppp) outliers start: 22 outliers final: 15 residues processed: 141 average time/residue: 0.2105 time to fit residues: 44.1505 Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11205 Z= 0.248 Angle : 0.562 8.956 15204 Z= 0.280 Chirality : 0.040 0.137 1811 Planarity : 0.004 0.055 1909 Dihedral : 8.804 76.609 1715 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.85 % Allowed : 17.71 % Favored : 80.44 % 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: 0.42 (0.23), residues: 1439 helix: 1.43 (0.18), residues: 863 sheet: -1.56 (0.56), residues: 84 loop : -1.47 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 300 HIS 0.002 0.000 HIS A 351 PHE 0.010 0.001 PHE A 109 TYR 0.020 0.002 TYR A 381 ARG 0.001 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 75 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6678 (ptt) REVERT: C 130 ASN cc_start: 0.8357 (t0) cc_final: 0.8118 (t0) REVERT: B 109 LEU cc_start: 0.0630 (OUTLIER) cc_final: 0.0353 (pp) REVERT: B 282 MET cc_start: 0.8638 (tpp) cc_final: 0.8305 (tpp) REVERT: B 392 MET cc_start: 0.2618 (mtm) cc_final: 0.1905 (ppp) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.2166 time to fit residues: 43.3820 Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.0070 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 211 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11205 Z= 0.160 Angle : 0.534 9.359 15204 Z= 0.264 Chirality : 0.038 0.136 1811 Planarity : 0.004 0.055 1909 Dihedral : 8.608 76.578 1715 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.76 % Allowed : 17.97 % Favored : 80.26 % 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: 0.55 (0.23), residues: 1439 helix: 1.54 (0.18), residues: 858 sheet: -1.53 (0.60), residues: 75 loop : -1.41 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.019 0.002 TYR A 126 ARG 0.001 0.000 ARG B 504 ********************** 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 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7742 (tt) REVERT: C 75 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6684 (ptt) REVERT: C 130 ASN cc_start: 0.8318 (t0) cc_final: 0.8113 (t0) REVERT: B 109 LEU cc_start: 0.0803 (OUTLIER) cc_final: 0.0510 (pp) REVERT: B 282 MET cc_start: 0.8566 (tpp) cc_final: 0.8362 (tpp) REVERT: B 392 MET cc_start: 0.2468 (mtm) cc_final: 0.1990 (ppp) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.2089 time to fit residues: 42.2001 Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 99 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 211 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111131 restraints weight = 15528.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110563 restraints weight = 16830.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112230 restraints weight = 11709.840| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11205 Z= 0.163 Angle : 0.527 9.356 15204 Z= 0.262 Chirality : 0.038 0.136 1811 Planarity : 0.003 0.055 1909 Dihedral : 8.506 76.964 1715 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.67 % Allowed : 17.62 % Favored : 80.70 % 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: 0.61 (0.23), residues: 1439 helix: 1.59 (0.18), residues: 858 sheet: -1.52 (0.61), residues: 75 loop : -1.38 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.001 0.000 HIS A 451 PHE 0.012 0.001 PHE A 109 TYR 0.027 0.002 TYR A 126 ARG 0.001 0.000 ARG B 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.34 seconds wall clock time: 39 minutes 27.24 seconds (2367.24 seconds total)