Starting phenix.real_space_refine on Sat Aug 23 13:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zri_14915/08_2025/7zri_14915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zri_14915/08_2025/7zri_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_14915/08_2025/7zri_14915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zri_14915/08_2025/7zri_14915.map" model { file = "/net/cci-nas-00/data/ceres_data/7zri_14915/08_2025/7zri_14915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zri_14915/08_2025/7zri_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-2.0-5787/lib/python3.9/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: 2.81, per 1000 atoms: 0.26 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: 0.99 Conformation dependent library (CDL) restraints added in 590.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 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: 1.88 Time building geometry restraints manager: 1.33 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- 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= 0.338 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (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 covalent geometry : bond 0.00588 (11205) covalent geometry : angle 0.91908 (15204) hydrogen bonds : bond 0.10685 ( 654) hydrogen bonds : angle 5.29085 ( 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 : 0.430 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: 0.0912 time to fit residues: 19.9744 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 : 0.418 ------------------------------------------------------------------------------- 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... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106896 restraints weight = 15682.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105273 restraints weight = 13414.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105937 restraints weight = 10859.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106263 restraints weight = 9540.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106414 restraints weight = 8569.887| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11205 Z= 0.199 Angle : 0.597 6.317 15204 Z= 0.305 Chirality : 0.042 0.244 1811 Planarity : 0.004 0.056 1909 Dihedral : 11.497 73.658 1715 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.62 % Allowed : 9.07 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1439 helix: 0.67 (0.18), residues: 871 sheet: -1.64 (0.55), residues: 87 loop : -1.89 (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 0.015 0.001 PHE A 354 TRP 0.021 0.001 TRP A 176 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00469 (11205) covalent geometry : angle 0.59750 (15204) hydrogen bonds : bond 0.03982 ( 654) hydrogen bonds : angle 4.61003 ( 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 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.262 Fit side-chains REVERT: A 176 TRP cc_start: 0.7254 (m-10) cc_final: 0.6908 (m-10) REVERT: C 130 ASN cc_start: 0.8390 (t0) cc_final: 0.8082 (t0) REVERT: B 469 MET cc_start: 0.7691 (tmm) cc_final: 0.7379 (ttt) outliers start: 7 outliers final: 6 residues processed: 130 average time/residue: 0.0912 time to fit residues: 18.0940 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3847 r_free = 0.3847 target = 0.150397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109860 restraints weight = 15744.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109228 restraints weight = 14776.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110770 restraints weight = 10673.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110665 restraints weight = 7915.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110893 restraints weight = 7690.519| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11205 Z= 0.107 Angle : 0.526 8.263 15204 Z= 0.263 Chirality : 0.039 0.148 1811 Planarity : 0.004 0.055 1909 Dihedral : 10.485 72.441 1715 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.88 % Allowed : 12.42 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1439 helix: 1.18 (0.18), residues: 860 sheet: -1.61 (0.54), residues: 84 loop : -1.67 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.018 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.009 0.001 TRP C 32 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00236 (11205) covalent geometry : angle 0.52562 (15204) hydrogen bonds : bond 0.03404 ( 654) hydrogen bonds : angle 4.35358 ( 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: 10 poor density : 129 time to evaluate : 0.286 Fit side-chains REVERT: A 176 TRP cc_start: 0.7200 (m-10) cc_final: 0.6675 (m-10) REVERT: A 352 ASP cc_start: 0.9125 (t0) cc_final: 0.8751 (t0) REVERT: C 64 TYR cc_start: 0.8732 (m-80) cc_final: 0.8511 (m-10) outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 0.0678 time to fit residues: 14.4628 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108308 restraints weight = 15785.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108522 restraints weight = 15845.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110026 restraints weight = 9993.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109909 restraints weight = 6937.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109966 restraints weight = 6889.457| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11205 Z= 0.135 Angle : 0.531 8.718 15204 Z= 0.267 Chirality : 0.039 0.135 1811 Planarity : 0.004 0.054 1909 Dihedral : 9.964 73.477 1715 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.97 % Allowed : 14.10 % 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 aren not related in a simple way. whole: 0.20 (0.22), residues: 1439 helix: 1.24 (0.18), residues: 867 sheet: -1.70 (0.53), residues: 84 loop : -1.56 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 89 TYR 0.019 0.002 TYR A 381 PHE 0.009 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 covalent geometry : bond 0.00314 (11205) covalent geometry : angle 0.53139 (15204) hydrogen bonds : bond 0.03436 ( 654) hydrogen bonds : angle 4.29375 ( 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 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.312 Fit side-chains REVERT: A 176 TRP cc_start: 0.7224 (m-10) cc_final: 0.6749 (m-10) REVERT: C 130 ASN cc_start: 0.8310 (t0) cc_final: 0.8031 (t0) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.0850 time to fit residues: 17.5174 Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 C residue 34 PHE 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: 0.8980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109743 restraints weight = 15603.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109804 restraints weight = 16266.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110970 restraints weight = 10533.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111112 restraints weight = 7369.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111182 restraints weight = 7296.333| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1429 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= 0.117 Angle : 0.515 8.929 15204 Z= 0.258 Chirality : 0.039 0.135 1811 Planarity : 0.003 0.055 1909 Dihedral : 9.559 73.800 1715 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.15 % Allowed : 15.15 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.23), residues: 1439 helix: 1.39 (0.18), residues: 861 sheet: -1.76 (0.53), residues: 84 loop : -1.45 (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 527 TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00267 (11205) covalent geometry : angle 0.51468 (15204) hydrogen bonds : bond 0.03328 ( 654) hydrogen bonds : angle 4.22065 ( 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: 13 poor density : 119 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7315 (m-10) cc_final: 0.6780 (m-10) REVERT: C 130 ASN cc_start: 0.8293 (t0) cc_final: 0.8018 (t0) outliers start: 13 outliers final: 11 residues processed: 130 average time/residue: 0.0837 time to fit residues: 16.6342 Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 D residue 7 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.0980 chunk 119 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111578 restraints weight = 15770.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111306 restraints weight = 15548.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112637 restraints weight = 10749.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112924 restraints weight = 7731.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113016 restraints weight = 7098.679| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11205 Z= 0.100 Angle : 0.501 9.219 15204 Z= 0.250 Chirality : 0.038 0.181 1811 Planarity : 0.003 0.054 1909 Dihedral : 9.106 73.516 1715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.59 % Allowed : 15.24 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.23), residues: 1439 helix: 1.49 (0.18), residues: 862 sheet: -1.68 (0.58), residues: 74 loop : -1.38 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.016 0.001 TYR A 381 PHE 0.009 0.001 PHE A 109 TRP 0.021 0.001 TRP A 300 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00220 (11205) covalent geometry : angle 0.50080 (15204) hydrogen bonds : bond 0.03154 ( 654) hydrogen bonds : angle 4.13340 ( 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: 18 poor density : 128 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9023 (t0) cc_final: 0.8781 (t70) REVERT: B 535 MET cc_start: 0.7454 (mmt) cc_final: 0.6565 (mmt) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.0825 time to fit residues: 18.2185 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 C residue 34 PHE 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 236 THR Chi-restraints excluded: chain B residue 433 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: 0.9990 chunk 69 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.151052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111610 restraints weight = 15617.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111943 restraints weight = 16558.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113369 restraints weight = 10055.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113502 restraints weight = 7457.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113318 restraints weight = 6965.015| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1600 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= 0.107 Angle : 0.511 9.196 15204 Z= 0.257 Chirality : 0.039 0.136 1811 Planarity : 0.003 0.054 1909 Dihedral : 8.840 73.902 1715 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.23), residues: 1439 helix: 1.54 (0.18), residues: 862 sheet: -1.53 (0.61), residues: 75 loop : -1.40 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.020 0.002 TYR A 126 PHE 0.010 0.001 PHE A 109 TRP 0.010 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00239 (11205) covalent geometry : angle 0.51080 (15204) hydrogen bonds : bond 0.03174 ( 654) hydrogen bonds : angle 4.12012 ( 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 144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7237 (m-90) cc_final: 0.6836 (m-90) REVERT: A 352 ASP cc_start: 0.9070 (t0) cc_final: 0.8789 (t70) REVERT: C 75 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6719 (ptt) REVERT: B 282 MET cc_start: 0.8680 (tpp) cc_final: 0.8294 (tpp) REVERT: B 535 MET cc_start: 0.7523 (mmt) cc_final: 0.6687 (mmt) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.0784 time to fit residues: 16.7620 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 10 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.0020 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112365 restraints weight = 15694.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112360 restraints weight = 16585.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114233 restraints weight = 10526.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114100 restraints weight = 7498.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114134 restraints weight = 7088.104| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11205 Z= 0.102 Angle : 0.512 9.439 15204 Z= 0.254 Chirality : 0.038 0.134 1811 Planarity : 0.003 0.055 1909 Dihedral : 8.589 74.262 1715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.41 % Allowed : 16.74 % 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 aren not related in a simple way. whole: 0.64 (0.23), residues: 1439 helix: 1.60 (0.18), residues: 859 sheet: -1.58 (0.60), residues: 75 loop : -1.34 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 504 TYR 0.023 0.001 TYR A 126 PHE 0.010 0.001 PHE A 109 TRP 0.009 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00225 (11205) covalent geometry : angle 0.51219 (15204) hydrogen bonds : bond 0.03122 ( 654) hydrogen bonds : angle 4.08101 ( 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 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7258 (m-90) cc_final: 0.6826 (m-90) REVERT: A 352 ASP cc_start: 0.9066 (t0) cc_final: 0.8776 (t70) REVERT: A 446 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7642 (tt) REVERT: C 75 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6725 (ptt) REVERT: B 282 MET cc_start: 0.8640 (tpp) cc_final: 0.8287 (tpp) REVERT: B 535 MET cc_start: 0.7518 (mmt) cc_final: 0.6669 (mmt) outliers start: 16 outliers final: 13 residues processed: 137 average time/residue: 0.0779 time to fit residues: 16.4228 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 : 0.240 ------------------------------------------------------------------------------- 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 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 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: 0.3980 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112607 restraints weight = 15597.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112755 restraints weight = 15813.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114247 restraints weight = 10811.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114369 restraints weight = 7826.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114447 restraints weight = 7283.041| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1709 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= 0.103 Angle : 0.516 9.409 15204 Z= 0.256 Chirality : 0.038 0.134 1811 Planarity : 0.003 0.054 1909 Dihedral : 8.381 75.384 1715 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 17.00 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.23), residues: 1439 helix: 1.62 (0.18), residues: 860 sheet: -1.45 (0.61), residues: 75 loop : -1.31 (0.27), residues: 504 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 0.014 0.001 PHE A 543 TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00229 (11205) covalent geometry : angle 0.51613 (15204) hydrogen bonds : bond 0.03144 ( 654) hydrogen bonds : angle 4.07582 ( 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 : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9076 (t0) cc_final: 0.8776 (t70) REVERT: A 446 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7710 (tt) REVERT: C 75 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6712 (ptt) REVERT: B 282 MET cc_start: 0.8602 (tpp) cc_final: 0.8231 (tpp) REVERT: B 392 MET cc_start: 0.2747 (mtm) cc_final: 0.2140 (ppp) REVERT: B 535 MET cc_start: 0.7545 (mmt) cc_final: 0.6740 (mmt) outliers start: 16 outliers final: 14 residues processed: 134 average time/residue: 0.0833 time to fit residues: 17.1482 Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 74 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 3 optimal weight: 0.0370 chunk 49 optimal weight: 0.0770 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 120 optimal weight: 0.2980 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113116 restraints weight = 15670.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113459 restraints weight = 16039.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115322 restraints weight = 9846.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114888 restraints weight = 6768.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115009 restraints weight = 7029.516| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1784 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= 0.098 Angle : 0.508 9.511 15204 Z= 0.253 Chirality : 0.038 0.134 1811 Planarity : 0.003 0.054 1909 Dihedral : 8.238 76.144 1715 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.32 % Allowed : 17.18 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.23), residues: 1439 helix: 1.66 (0.18), residues: 860 sheet: -1.40 (0.62), residues: 75 loop : -1.29 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.017 0.001 TYR A 381 PHE 0.010 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 covalent geometry : bond 0.00213 (11205) covalent geometry : angle 0.50794 (15204) hydrogen bonds : bond 0.03088 ( 654) hydrogen bonds : angle 4.05956 ( 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 140 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 352 ASP cc_start: 0.9076 (t0) cc_final: 0.8759 (t70) REVERT: A 446 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 543 PHE cc_start: 0.7560 (m-80) cc_final: 0.7326 (m-80) REVERT: C 75 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6718 (ptt) REVERT: B 282 MET cc_start: 0.8642 (tpp) cc_final: 0.8251 (tpp) REVERT: B 392 MET cc_start: 0.2579 (mtm) cc_final: 0.2068 (ppp) REVERT: B 535 MET cc_start: 0.7465 (mmt) cc_final: 0.6663 (mmt) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.0814 time to fit residues: 16.8669 Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 LEU 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 74 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110945 restraints weight = 15599.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111789 restraints weight = 16836.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113546 restraints weight = 11331.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112758 restraints weight = 8094.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113113 restraints weight = 7932.049| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11205 Z= 0.131 Angle : 0.534 9.379 15204 Z= 0.265 Chirality : 0.039 0.135 1811 Planarity : 0.004 0.068 1909 Dihedral : 8.316 78.477 1715 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.32 % Allowed : 17.18 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.23), residues: 1439 helix: 1.56 (0.18), residues: 865 sheet: -1.36 (0.63), residues: 75 loop : -1.33 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.020 0.002 TYR A 381 PHE 0.008 0.001 PHE A 543 TRP 0.008 0.001 TRP A 176 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00308 (11205) covalent geometry : angle 0.53445 (15204) hydrogen bonds : bond 0.03319 ( 654) hydrogen bonds : angle 4.13813 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.31 seconds wall clock time: 29 minutes 1.06 seconds (1741.06 seconds total)