Starting phenix.real_space_refine on Fri Jul 3 05:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_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_14915/07_2026/7zri_14915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2026/7zri_14915.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.41, per 1000 atoms: 0.22 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: 0.82 Conformation dependent library (CDL) restraints added in 502.7 milliseconds 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: 0.31 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: 1.49 Time building geometry restraints manager: 1.15 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: 5823 16.81 - 33.63: 654 33.63 - 50.44: 162 50.44 - 67.25: 45 67.25 - 84.06: 11 Dihedral angle restraints: 6695 sinusoidal: 2589 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 6692 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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= 0.338 Angle : 0.919 9.799 15204 Z= 0.465 Chirality : 0.047 0.211 1811 Planarity : 0.006 0.064 1909 Dihedral : 15.751 84.064 4057 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 172 TYR 0.033 0.002 TYR A 126 PHE 0.029 0.002 PHE A 260 TRP 0.016 0.002 TRP C 32 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.34 (11205) covalent geometry : angle 0.91908 / 0.47 (15204) hydrogen bonds : bond 0.10685 / 6.75 ( 654) hydrogen bonds : angle 5.29085 / 3.78 ( 1923) *********************** 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 : 0.286 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: 0.0802 time to fit residues: 17.7013 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 : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 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 = 0.3807 r_free = 0.3807 target = 0.147039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106828 restraints weight = 15683.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105389 restraints weight = 12172.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105730 restraints weight = 11011.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106049 restraints weight = 9589.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106536 restraints weight = 8715.342| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11205 Z= 0.197 Angle : 0.599 6.394 15204 Z= 0.306 Chirality : 0.042 0.218 1811 Planarity : 0.004 0.055 1909 Dihedral : 10.039 59.561 1675 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.79 % Allowed : 9.34 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1439 helix: 0.67 (0.18), residues: 871 sheet: -1.62 (0.55), residues: 87 loop : -1.88 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.023 0.002 TYR A 381 PHE 0.016 0.001 PHE A 354 TRP 0.011 0.001 TRP C 32 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (11205) covalent geometry : angle 0.59883 / 0.31 (15204) hydrogen bonds : bond 0.03995 / 2.71 ( 654) hydrogen bonds : angle 4.60439 / 3.31 ( 1923) *********************** 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 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.320 Fit side-chains REVERT: A 176 TRP cc_start: 0.7276 (m-10) cc_final: 0.6959 (m-10) REVERT: A 352 ASP cc_start: 0.9166 (t0) cc_final: 0.8801 (t0) REVERT: C 130 ASN cc_start: 0.8377 (t0) cc_final: 0.8063 (t0) REVERT: B 469 MET cc_start: 0.7705 (tmm) cc_final: 0.7401 (ttt) outliers start: 9 outliers final: 6 residues processed: 132 average time/residue: 0.0867 time to fit residues: 17.3864 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 43 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 GLN C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.150018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109834 restraints weight = 15738.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109812 restraints weight = 15812.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111432 restraints weight = 10143.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111295 restraints weight = 6967.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111347 restraints weight = 7293.735| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11205 Z= 0.111 Angle : 0.527 7.830 15204 Z= 0.263 Chirality : 0.039 0.151 1811 Planarity : 0.004 0.055 1909 Dihedral : 8.826 59.187 1675 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.79 % Allowed : 12.60 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1439 helix: 1.16 (0.18), residues: 860 sheet: -1.52 (0.53), residues: 86 loop : -1.69 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.019 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.010 0.001 TRP C 32 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11205) covalent geometry : angle 0.52688 / 0.26 (15204) hydrogen bonds : bond 0.03407 / 2.31 ( 654) hydrogen bonds : angle 4.35399 / 3.13 ( 1923) *********************** 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 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.248 Fit side-chains REVERT: A 176 TRP cc_start: 0.7224 (m-10) cc_final: 0.6881 (m-10) REVERT: A 352 ASP cc_start: 0.9157 (t0) cc_final: 0.8777 (t0) outliers start: 9 outliers final: 8 residues processed: 137 average time/residue: 0.0778 time to fit residues: 16.3985 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 C residue 154 GLN Chi-restraints excluded: chain B residue 12 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 40 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 103 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 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 = 0.3836 r_free = 0.3836 target = 0.149604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109304 restraints weight = 15775.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109521 restraints weight = 14648.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111268 restraints weight = 9921.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110893 restraints weight = 7330.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111177 restraints weight = 7090.383| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1323 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= 0.118 Angle : 0.520 8.874 15204 Z= 0.261 Chirality : 0.039 0.135 1811 Planarity : 0.004 0.054 1909 Dihedral : 8.183 59.667 1675 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.15 % Allowed : 13.92 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1439 helix: 1.29 (0.18), residues: 867 sheet: -1.68 (0.52), residues: 84 loop : -1.57 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.019 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.008 0.001 TRP C 32 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11205) covalent geometry : angle 0.51984 / 0.26 (15204) hydrogen bonds : bond 0.03343 / 2.26 ( 654) hydrogen bonds : angle 4.25957 / 3.07 ( 1923) *********************** 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 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.401 Fit side-chains REVERT: A 176 TRP cc_start: 0.7254 (m-10) cc_final: 0.6780 (m-10) REVERT: A 352 ASP cc_start: 0.9158 (t0) cc_final: 0.8768 (t0) REVERT: C 154 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7577 (tp40) outliers start: 13 outliers final: 10 residues processed: 137 average time/residue: 0.0855 time to fit residues: 18.2283 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 : 0.559 ------------------------------------------------------------------------------- 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 34 PHE Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 74 ILE 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 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 119 optimal weight: 20.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 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 = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109882 restraints weight = 15582.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110133 restraints weight = 14401.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111846 restraints weight = 9834.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111328 restraints weight = 7185.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111483 restraints weight = 7450.794| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11205 Z= 0.110 Angle : 0.510 8.859 15204 Z= 0.256 Chirality : 0.039 0.135 1811 Planarity : 0.003 0.054 1909 Dihedral : 7.795 59.791 1675 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.32 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1439 helix: 1.44 (0.18), residues: 861 sheet: -1.69 (0.53), residues: 84 loop : -1.46 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 68 TYR 0.018 0.001 TYR A 381 PHE 0.008 0.001 PHE A 109 TRP 0.015 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11205) covalent geometry : angle 0.50998 / 0.26 (15204) hydrogen bonds : bond 0.03270 / 2.21 ( 654) hydrogen bonds : angle 4.19149 / 3.02 ( 1923) *********************** 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 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7339 (m-10) cc_final: 0.6832 (m-10) REVERT: C 154 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7638 (tp40) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 0.0871 time to fit residues: 17.4086 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 34 PHE Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 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 126 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 135 optimal weight: 0.0060 chunk 124 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110757 restraints weight = 15791.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111071 restraints weight = 15673.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112978 restraints weight = 9921.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112382 restraints weight = 7036.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112545 restraints weight = 7444.265| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1467 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= 0.105 Angle : 0.505 9.227 15204 Z= 0.252 Chirality : 0.038 0.135 1811 Planarity : 0.003 0.054 1909 Dihedral : 7.542 59.157 1675 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.76 % Allowed : 15.42 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1439 helix: 1.48 (0.18), residues: 862 sheet: -1.63 (0.59), residues: 74 loop : -1.40 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.017 0.001 TYR A 381 PHE 0.009 0.001 PHE A 109 TRP 0.009 0.001 TRP A 300 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11205) covalent geometry : angle 0.50461 / 0.25 (15204) hydrogen bonds : bond 0.03195 / 2.16 ( 654) hydrogen bonds : angle 4.15032 / 2.99 ( 1923) *********************** 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 146 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9074 (t0) cc_final: 0.8813 (t0) outliers start: 20 outliers final: 16 residues processed: 143 average time/residue: 0.0807 time to fit residues: 17.8131 Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 85 SER 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 74 ILE Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 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 = 0.3851 r_free = 0.3851 target = 0.150907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111292 restraints weight = 15616.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110976 restraints weight = 16915.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112893 restraints weight = 10874.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112754 restraints weight = 7668.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112831 restraints weight = 7329.586| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11205 Z= 0.106 Angle : 0.512 9.255 15204 Z= 0.256 Chirality : 0.039 0.135 1811 Planarity : 0.003 0.054 1909 Dihedral : 7.327 57.006 1675 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.50 % Allowed : 16.48 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1439 helix: 1.49 (0.18), residues: 868 sheet: -1.47 (0.60), residues: 74 loop : -1.42 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.021 0.002 TYR A 126 PHE 0.009 0.001 PHE A 109 TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11205) covalent geometry : angle 0.51233 / 0.26 (15204) hydrogen bonds : bond 0.03178 / 2.15 ( 654) hydrogen bonds : angle 4.12057 / 2.97 ( 1923) *********************** 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 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9077 (t0) cc_final: 0.8797 (t0) REVERT: B 282 MET cc_start: 0.8685 (tpp) cc_final: 0.8423 (tpp) outliers start: 17 outliers final: 15 residues processed: 137 average time/residue: 0.0860 time to fit residues: 17.9044 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL 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 74 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109651 restraints weight = 15727.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109072 restraints weight = 17532.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111229 restraints weight = 11300.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111045 restraints weight = 7684.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111144 restraints weight = 7373.376| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11205 Z= 0.126 Angle : 0.527 9.250 15204 Z= 0.264 Chirality : 0.039 0.154 1811 Planarity : 0.003 0.054 1909 Dihedral : 7.201 56.854 1675 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 16.83 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1439 helix: 1.47 (0.18), residues: 871 sheet: -1.56 (0.61), residues: 75 loop : -1.41 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.019 0.002 TYR A 381 PHE 0.008 0.001 PHE A 109 TRP 0.006 0.001 TRP B 71 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11205) covalent geometry : angle 0.52735 / 0.26 (15204) hydrogen bonds : bond 0.03295 / 2.23 ( 654) hydrogen bonds : angle 4.15341 / 3.00 ( 1923) *********************** 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9100 (t0) cc_final: 0.8808 (t0) REVERT: C 130 ASN cc_start: 0.8221 (t0) cc_final: 0.7997 (t0) REVERT: B 282 MET cc_start: 0.8673 (tpp) cc_final: 0.8266 (tpp) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.0805 time to fit residues: 16.1318 Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 85 SER 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 127 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110084 restraints weight = 15639.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110206 restraints weight = 16101.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111851 restraints weight = 9980.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111582 restraints weight = 6836.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111712 restraints weight = 7148.707| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11205 Z= 0.118 Angle : 0.526 9.256 15204 Z= 0.262 Chirality : 0.039 0.135 1811 Planarity : 0.003 0.054 1909 Dihedral : 7.033 56.686 1675 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.41 % Allowed : 16.56 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1439 helix: 1.51 (0.18), residues: 867 sheet: -1.43 (0.62), residues: 75 loop : -1.37 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.019 0.001 TYR A 126 PHE 0.009 0.001 PHE A 109 TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11205) covalent geometry : angle 0.52588 / 0.26 (15204) hydrogen bonds : bond 0.03261 / 2.20 ( 654) hydrogen bonds : angle 4.12754 / 2.97 ( 1923) *********************** 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 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9107 (t0) cc_final: 0.8826 (t0) REVERT: A 446 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7775 (tt) REVERT: C 130 ASN cc_start: 0.8222 (t0) cc_final: 0.8010 (t0) REVERT: B 282 MET cc_start: 0.8622 (tpp) cc_final: 0.8294 (tpp) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.0785 time to fit residues: 16.4200 Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 A residue 446 LEU 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 74 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111941 restraints weight = 15738.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112355 restraints weight = 15536.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113938 restraints weight = 9899.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113752 restraints weight = 6723.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113816 restraints weight = 6671.539| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1698 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= 0.101 Angle : 0.515 9.548 15204 Z= 0.257 Chirality : 0.039 0.143 1811 Planarity : 0.003 0.054 1909 Dihedral : 6.805 56.432 1675 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.32 % Allowed : 16.65 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1439 helix: 1.61 (0.18), residues: 862 sheet: -1.36 (0.63), residues: 75 loop : -1.35 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.027 0.002 TYR A 126 PHE 0.011 0.001 PHE A 109 TRP 0.007 0.001 TRP B 186 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11205) covalent geometry : angle 0.51528 / 0.26 (15204) hydrogen bonds : bond 0.03138 / 2.12 ( 654) hydrogen bonds : angle 4.08473 / 2.94 ( 1923) ********************** 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7688 (tt) REVERT: C 64 TYR cc_start: 0.8650 (m-10) cc_final: 0.8449 (m-10) REVERT: B 282 MET cc_start: 0.8570 (tpp) cc_final: 0.8306 (tpp) REVERT: B 392 MET cc_start: 0.2592 (mtm) cc_final: 0.2097 (ppp) outliers start: 15 outliers final: 14 residues processed: 134 average time/residue: 0.0804 time to fit residues: 16.7162 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 A residue 446 LEU 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 74 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112552 restraints weight = 15601.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112958 restraints weight = 16022.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114433 restraints weight = 9643.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114271 restraints weight = 6742.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114298 restraints weight = 6731.742| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1765 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= 0.102 Angle : 0.512 9.432 15204 Z= 0.255 Chirality : 0.038 0.134 1811 Planarity : 0.003 0.055 1909 Dihedral : 6.630 57.481 1675 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 16.56 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1439 helix: 1.65 (0.18), residues: 863 sheet: -1.31 (0.63), residues: 75 loop : -1.27 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.022 0.002 TYR A 126 PHE 0.011 0.001 PHE A 109 TRP 0.006 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11205) covalent geometry : angle 0.51224 / 0.26 (15204) hydrogen bonds : bond 0.03109 / 2.10 ( 654) hydrogen bonds : angle 4.05829 / 2.92 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.60 seconds wall clock time: 29 minutes 43.80 seconds (1783.80 seconds total)