Starting phenix.real_space_refine on Sat Dec 28 22:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpw_60365/12_2024/8zpw_60365_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 38 5.16 5 C 5961 2.51 5 N 1480 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5431 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 629} Chain breaks: 6 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3775 Classifications: {'peptide': 477} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 454} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.63, per 1000 atoms: 0.61 Number of scatterers: 9252 At special positions: 0 Unit cell: (104.775, 102.3, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 38 16.00 O 1772 8.00 N 1480 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 579 " - pdb=" SG CYS B 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS B 61 " distance=2.04 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 46.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.278A pdb=" N THR A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 278 through 292 removed outlier: 3.755A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 349 through 368 removed outlier: 3.675A pdb=" N MET A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.761A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 479 removed outlier: 4.110A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.777A pdb=" N SER A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.734A pdb=" N ALA A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.600A pdb=" N ASN B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.828A pdb=" N LYS B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 4.048A pdb=" N GLU B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.556A pdb=" N GLU B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.887A pdb=" N ILE B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.353A pdb=" N ALA B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 Proline residue: B 275 - end of helix Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.785A pdb=" N GLY B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 382 through 391 removed outlier: 4.742A pdb=" N ASP B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 425 removed outlier: 3.672A pdb=" N LYS B 410 " --> pdb=" O CYS B 406 " (cutoff:3.500A) Proline residue: B 414 - end of helix removed outlier: 3.600A pdb=" N ASN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.545A pdb=" N LEU B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.838A pdb=" N GLU A 59 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 66 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 452 removed outlier: 6.773A pdb=" N GLU A 457 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 663 removed outlier: 3.609A pdb=" N LEU A 659 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 661 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE A 680 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 685 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE A 739 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 687 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 668 through 669 removed outlier: 6.212A pdb=" N ILE A 675 " --> pdb=" O GLN A 751 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS A 753 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A 677 " --> pdb=" O LYS A 753 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 750 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 796 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE A 752 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 775 through 777 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.409A pdb=" N VAL B 35 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP B 89 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 53 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 88 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU B 55 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 143 through 145 removed outlier: 6.219A pdb=" N ALA B 144 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 206 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 212 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 289 through 294 Processing sheet with id=AB5, first strand: chain 'B' and resid 379 through 381 removed outlier: 4.215A pdb=" N ASP B 436 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP B 396 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA B 433 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 398 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 435 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 400 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 397 " --> pdb=" O TYR B 456 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2964 1.34 - 1.46: 2177 1.46 - 1.58: 4282 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9486 Sorted by residual: bond pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLN B 24 " pdb=" CA GLN B 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C5 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12369 1.14 - 2.28: 388 2.28 - 3.42: 79 3.42 - 4.56: 35 4.56 - 5.70: 4 Bond angle restraints: 12875 Sorted by residual: angle pdb=" C ASP A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.86e+00 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 118.46 -4.36 2.00e+00 2.50e-01 4.75e+00 angle pdb=" CA CYS B 61 " pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " ideal model delta sigma weight residual 114.40 119.18 -4.78 2.30e+00 1.89e-01 4.32e+00 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.70e+00 3.46e-01 4.16e+00 angle pdb=" N ALA B 26 " pdb=" CA ALA B 26 " pdb=" CB ALA B 26 " ideal model delta sigma weight residual 113.65 110.73 2.92 1.47e+00 4.63e-01 3.94e+00 ... (remaining 12870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5085 17.49 - 34.97: 469 34.97 - 52.46: 106 52.46 - 69.95: 28 69.95 - 87.44: 13 Dihedral angle restraints: 5701 sinusoidal: 2334 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS A 644 " pdb=" SG CYS A 644 " pdb=" SG CYS B 61 " pdb=" CB CYS B 61 " ideal model delta sinusoidal sigma weight residual -86.00 -120.28 34.28 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA CYS B 61 " pdb=" C CYS B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU B 25 " pdb=" CG GLU B 25 " pdb=" CD GLU B 25 " pdb=" OE1 GLU B 25 " ideal model delta sinusoidal sigma weight residual 0.00 -87.44 87.44 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 839 0.027 - 0.054: 366 0.054 - 0.081: 101 0.081 - 0.108: 62 0.108 - 0.135: 42 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA ILE A 795 " pdb=" N ILE A 795 " pdb=" C ILE A 795 " pdb=" CB ILE A 795 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE A 777 " pdb=" N ILE A 777 " pdb=" C ILE A 777 " pdb=" CB ILE A 777 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 587 " pdb=" N ILE A 587 " pdb=" C ILE A 587 " pdb=" CB ILE A 587 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1407 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 443 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.36e+00 pdb=" NE ARG B 443 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 443 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 443 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 443 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 74 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO A 75 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 437 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LEU A 437 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU A 437 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 438 " 0.008 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 141 2.61 - 3.19: 8641 3.19 - 3.76: 14847 3.76 - 4.33: 21416 4.33 - 4.90: 34958 Nonbonded interactions: 80003 Sorted by model distance: nonbonded pdb=" O ALA A 338 " pdb=" OG SER A 413 " model vdw 2.043 3.040 nonbonded pdb=" O ARG A 137 " pdb=" OG SER A 141 " model vdw 2.044 3.040 nonbonded pdb=" NH1 ARG A 635 " pdb=" O LYS B 297 " model vdw 2.071 3.120 nonbonded pdb=" OE1 GLU A 236 " pdb=" OH TYR A 510 " model vdw 2.102 3.040 nonbonded pdb=" OD1 ASP A 74 " pdb=" OG1 THR A 76 " model vdw 2.116 3.040 ... (remaining 79998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9486 Z= 0.179 Angle : 0.526 5.703 12875 Z= 0.272 Chirality : 0.040 0.135 1410 Planarity : 0.004 0.071 1664 Dihedral : 15.061 87.435 3513 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.19 % Allowed : 18.06 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1129 helix: 2.00 (0.25), residues: 460 sheet: 0.42 (0.49), residues: 128 loop : -0.13 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 374 HIS 0.009 0.001 HIS A 747 PHE 0.014 0.001 PHE A 425 TYR 0.018 0.001 TYR A 732 ARG 0.010 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.165 Fit side-chains REVERT: A 189 MET cc_start: 0.8426 (tpp) cc_final: 0.8031 (mmt) REVERT: B 198 ASP cc_start: 0.7588 (m-30) cc_final: 0.7178 (p0) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 1.0971 time to fit residues: 120.1601 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 476 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.0470 chunk 47 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS B 82 ASN B 289 ASN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9486 Z= 0.170 Angle : 0.508 6.836 12875 Z= 0.268 Chirality : 0.042 0.158 1410 Planarity : 0.004 0.035 1664 Dihedral : 5.146 54.412 1316 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 15.58 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1129 helix: 2.11 (0.25), residues: 461 sheet: 0.34 (0.47), residues: 126 loop : -0.18 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.005 0.001 HIS A 747 PHE 0.018 0.001 PHE A 425 TYR 0.017 0.001 TYR A 698 ARG 0.004 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8373 (tpp) cc_final: 0.7971 (mmt) REVERT: A 322 MET cc_start: 0.8007 (mtm) cc_final: 0.7806 (mtp) REVERT: A 669 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6832 (tpp) REVERT: A 702 LEU cc_start: 0.8718 (tt) cc_final: 0.8336 (tm) REVERT: A 732 TYR cc_start: 0.7782 (p90) cc_final: 0.7563 (p90) REVERT: A 742 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8396 (mmt-90) REVERT: A 780 HIS cc_start: 0.7218 (m-70) cc_final: 0.6686 (m90) REVERT: B 76 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: B 79 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8385 (m) REVERT: B 198 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7275 (p0) outliers start: 18 outliers final: 6 residues processed: 123 average time/residue: 1.0646 time to fit residues: 142.2237 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 747 HIS B 43 ASN B 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9486 Z= 0.386 Angle : 0.585 8.137 12875 Z= 0.305 Chirality : 0.045 0.197 1410 Planarity : 0.004 0.036 1664 Dihedral : 4.802 40.328 1301 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.58 % Allowed : 16.77 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1129 helix: 1.94 (0.24), residues: 448 sheet: 0.21 (0.45), residues: 126 loop : -0.34 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.008 0.002 HIS B 485 PHE 0.020 0.002 PHE A 591 TYR 0.015 0.002 TYR A 418 ARG 0.004 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 654 GLU cc_start: 0.7676 (pp20) cc_final: 0.7357 (pp20) REVERT: A 702 LEU cc_start: 0.8740 (tt) cc_final: 0.8347 (tm) REVERT: A 780 HIS cc_start: 0.7272 (m-70) cc_final: 0.6686 (m90) REVERT: B 79 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8412 (m) REVERT: B 198 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7307 (p0) REVERT: B 231 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (ttmm) REVERT: B 395 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (mtpm) outliers start: 26 outliers final: 8 residues processed: 106 average time/residue: 1.1624 time to fit residues: 133.4355 Evaluate side-chains 89 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 HIS A 747 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9486 Z= 0.163 Angle : 0.491 7.451 12875 Z= 0.256 Chirality : 0.041 0.152 1410 Planarity : 0.003 0.037 1664 Dihedral : 4.023 18.739 1299 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.48 % Allowed : 17.26 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1129 helix: 1.98 (0.25), residues: 461 sheet: 0.49 (0.47), residues: 122 loop : -0.19 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 PHE 0.016 0.001 PHE A 425 TYR 0.022 0.001 TYR A 732 ARG 0.005 0.001 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8359 (tpp) cc_final: 0.7942 (mmt) REVERT: A 322 MET cc_start: 0.8088 (mtm) cc_final: 0.7865 (mtp) REVERT: A 702 LEU cc_start: 0.8752 (tt) cc_final: 0.8380 (tm) REVERT: A 780 HIS cc_start: 0.7205 (m-70) cc_final: 0.6687 (m90) REVERT: B 76 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 79 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8390 (m) REVERT: B 198 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7246 (p0) REVERT: B 271 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7845 (tm-30) REVERT: B 395 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8489 (mtpm) outliers start: 25 outliers final: 10 residues processed: 113 average time/residue: 1.0580 time to fit residues: 130.0121 Evaluate side-chains 91 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9486 Z= 0.279 Angle : 0.537 7.526 12875 Z= 0.278 Chirality : 0.043 0.165 1410 Planarity : 0.004 0.040 1664 Dihedral : 4.102 17.965 1299 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.48 % Allowed : 18.15 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1129 helix: 1.91 (0.24), residues: 456 sheet: 0.47 (0.47), residues: 122 loop : -0.22 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 PHE 0.017 0.001 PHE A 465 TYR 0.023 0.001 TYR A 732 ARG 0.005 0.001 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8341 (tpp) cc_final: 0.7903 (mmt) REVERT: A 352 ASP cc_start: 0.8543 (m-30) cc_final: 0.8330 (t0) REVERT: A 702 LEU cc_start: 0.8718 (tt) cc_final: 0.8327 (tm) REVERT: A 780 HIS cc_start: 0.7176 (m-70) cc_final: 0.6703 (m90) REVERT: B 76 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: B 79 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 198 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7283 (p0) REVERT: B 231 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8246 (ttmm) REVERT: B 271 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7868 (tm-30) REVERT: B 395 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8506 (mtpm) outliers start: 25 outliers final: 8 residues processed: 104 average time/residue: 1.2473 time to fit residues: 140.9484 Evaluate side-chains 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9486 Z= 0.177 Angle : 0.492 7.134 12875 Z= 0.255 Chirality : 0.041 0.154 1410 Planarity : 0.003 0.040 1664 Dihedral : 3.945 19.028 1299 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.08 % Allowed : 19.15 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1129 helix: 1.95 (0.25), residues: 462 sheet: 0.55 (0.47), residues: 122 loop : -0.13 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 PHE 0.016 0.001 PHE A 465 TYR 0.022 0.001 TYR A 732 ARG 0.006 0.001 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8332 (tpp) cc_final: 0.7919 (mmt) REVERT: A 322 MET cc_start: 0.8069 (mtm) cc_final: 0.7827 (mtp) REVERT: A 352 ASP cc_start: 0.8497 (m-30) cc_final: 0.8280 (t0) REVERT: A 702 LEU cc_start: 0.8714 (tt) cc_final: 0.8336 (tm) REVERT: A 742 ARG cc_start: 0.8802 (mtt90) cc_final: 0.8346 (mmt-90) REVERT: A 780 HIS cc_start: 0.7029 (m-70) cc_final: 0.6597 (m90) REVERT: B 76 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: B 79 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 198 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7194 (p0) REVERT: B 231 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8127 (ttmm) REVERT: B 271 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7862 (tm-30) REVERT: B 395 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8506 (mtpm) outliers start: 21 outliers final: 8 residues processed: 103 average time/residue: 1.0736 time to fit residues: 120.1618 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 373 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 0.0570 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9486 Z= 0.242 Angle : 0.518 7.728 12875 Z= 0.267 Chirality : 0.042 0.156 1410 Planarity : 0.003 0.041 1664 Dihedral : 4.047 18.135 1299 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.28 % Allowed : 19.25 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1129 helix: 1.94 (0.25), residues: 454 sheet: 0.53 (0.47), residues: 122 loop : -0.16 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 364 HIS 0.006 0.001 HIS A 747 PHE 0.017 0.001 PHE A 465 TYR 0.022 0.001 TYR A 732 ARG 0.004 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8319 (tpp) cc_final: 0.7879 (mmt) REVERT: A 322 MET cc_start: 0.8105 (mtm) cc_final: 0.7844 (mtp) REVERT: A 352 ASP cc_start: 0.8564 (m-30) cc_final: 0.8343 (t0) REVERT: A 702 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8350 (tm) REVERT: A 742 ARG cc_start: 0.8811 (mtt90) cc_final: 0.8325 (mmt-90) REVERT: A 780 HIS cc_start: 0.7066 (m-70) cc_final: 0.6642 (m90) REVERT: B 76 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 79 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 135 MET cc_start: 0.9167 (mmt) cc_final: 0.8822 (mmt) REVERT: B 198 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7200 (p0) REVERT: B 271 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7888 (tm-30) REVERT: B 395 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8502 (mtpm) outliers start: 23 outliers final: 10 residues processed: 104 average time/residue: 1.1867 time to fit residues: 134.8529 Evaluate side-chains 97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9007 > 50: distance: 41 - 61: 27.794 distance: 46 - 68: 31.301 distance: 50 - 77: 36.353 distance: 55 - 61: 29.486 distance: 56 - 85: 29.456 distance: 61 - 62: 56.366 distance: 62 - 63: 61.074 distance: 62 - 65: 45.528 distance: 63 - 64: 57.611 distance: 63 - 68: 55.425 distance: 64 - 96: 21.785 distance: 65 - 66: 20.288 distance: 65 - 67: 39.004 distance: 68 - 69: 51.644 distance: 69 - 70: 30.628 distance: 69 - 72: 20.346 distance: 70 - 71: 32.887 distance: 70 - 77: 44.174 distance: 71 - 104: 3.578 distance: 72 - 73: 10.952 distance: 73 - 74: 19.858 distance: 74 - 75: 50.832 distance: 75 - 76: 33.401 distance: 77 - 78: 3.105 distance: 78 - 79: 20.416 distance: 78 - 81: 39.746 distance: 79 - 80: 22.162 distance: 79 - 85: 26.227 distance: 80 - 113: 3.892 distance: 85 - 86: 14.461 distance: 86 - 87: 9.195 distance: 86 - 89: 14.072 distance: 87 - 96: 47.915 distance: 89 - 90: 8.932 distance: 90 - 91: 25.041 distance: 90 - 92: 21.652 distance: 91 - 93: 23.651 distance: 92 - 94: 9.875 distance: 93 - 95: 17.274 distance: 94 - 95: 21.606 distance: 96 - 97: 14.651 distance: 97 - 98: 42.028 distance: 97 - 100: 11.182 distance: 100 - 101: 19.006 distance: 101 - 102: 17.851 distance: 101 - 103: 29.518 distance: 104 - 105: 41.021 distance: 105 - 106: 37.634 distance: 105 - 108: 31.770 distance: 106 - 113: 32.190 distance: 108 - 109: 44.334 distance: 109 - 110: 58.006 distance: 110 - 111: 28.449 distance: 111 - 112: 44.062 distance: 113 - 114: 57.823 distance: 114 - 115: 12.505 distance: 115 - 116: 40.374 distance: 117 - 118: 39.815 distance: 118 - 119: 11.445 distance: 118 - 121: 17.833 distance: 119 - 120: 49.378 distance: 119 - 125: 9.801 distance: 121 - 122: 49.219 distance: 122 - 123: 4.038 distance: 122 - 124: 36.012 distance: 127 - 128: 41.167 distance: 127 - 130: 39.507 distance: 130 - 131: 56.208 distance: 131 - 134: 15.154 distance: 132 - 133: 20.621 distance: 132 - 136: 34.588 distance: 134 - 135: 61.694