Starting phenix.real_space_refine on Thu Nov 14 22:41:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilq_35540/11_2024/8ilq_35540.cif" } resolution = 4.3 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= 1.000 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 4850 2.51 5 N 1331 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7729 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3837 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 24, 'TRANS': 476} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3808 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 21, 'TRANS': 487} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.08, per 1000 atoms: 0.66 Number of scatterers: 7729 At special positions: 0 Unit cell: (189, 128.52, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 1469 8.00 N 1331 7.00 C 4850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 356 " - pdb=" SG CYS A 424 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 778 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 823 " distance=2.04 Simple disulfide: pdb=" SG CYS B 908 " - pdb=" SG CYS B 978 " distance=2.03 Simple disulfide: pdb=" SG CYS B 918 " - pdb=" SG CYS B 921 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 601 " - " ASN A 33 " " NAG B1101 " - " ASN B 914 " " NAG B1102 " - " ASN B 853 " " NAG B1103 " - " ASN B 936 " " NAG C 1 " - " ASN A 63 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 17 sheets defined 16.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.840A pdb=" N ASP A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.043A pdb=" N HIS A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.973A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.936A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.816A pdb=" N VAL A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 291 " --> pdb=" O CYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.397A pdb=" N GLU A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 451 through 465 removed outlier: 3.678A pdb=" N PHE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.638A pdb=" N THR A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.859A pdb=" N VAL A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 500 removed outlier: 3.955A pdb=" N ARG A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.893A pdb=" N LYS A 508 " --> pdb=" O CYS A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1054 removed outlier: 3.771A pdb=" N ILE B1037 " --> pdb=" O LEU B1033 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY B1047 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B1048 " --> pdb=" O LEU B1044 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B1050 " --> pdb=" O GLY B1046 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B1054 " --> pdb=" O LEU B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1063 removed outlier: 3.931A pdb=" N LYS B1059 " --> pdb=" O MET B1055 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 removed outlier: 6.531A pdb=" N LEU A 167 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.982A pdb=" N SER A 81 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 129 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.626A pdb=" N CYS A 327 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 335 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 228 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 383 removed outlier: 3.510A pdb=" N SER A 372 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 409 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 575 through 576 removed outlier: 3.788A pdb=" N VAL B 587 " --> pdb=" O SER B 575 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 602 through 603 removed outlier: 4.002A pdb=" N LYS B 621 " --> pdb=" O GLU B 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 635 through 637 removed outlier: 3.799A pdb=" N SER B 723 " --> pdb=" O GLU B 779 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 779 " --> pdb=" O SER B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 760 through 765 removed outlier: 3.684A pdb=" N THR B 763 " --> pdb=" O SER B 891 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 832 through 834 removed outlier: 3.966A pdb=" N GLU B 833 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 840 " --> pdb=" O GLU B 833 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 908 through 917 removed outlier: 3.824A pdb=" N THR B 909 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 928 " --> pdb=" O THR B 913 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 915 " --> pdb=" O LYS B 926 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS B 926 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 938 through 939 removed outlier: 3.888A pdb=" N PHE B 950 " --> pdb=" O ALA B 939 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 973 through 974 removed outlier: 3.520A pdb=" N CYS B 974 " --> pdb=" O VAL B 985 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 985 " --> pdb=" O CYS B 974 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 177 hydrogen bonds defined for protein. 465 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: 2.17 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2503 1.34 - 1.46: 1837 1.46 - 1.59: 3454 1.59 - 1.71: 0 1.71 - 1.83: 103 Bond restraints: 7897 Sorted by residual: bond pdb=" CA PRO A 449 " pdb=" C PRO A 449 " ideal model delta sigma weight residual 1.517 1.554 -0.037 1.46e-02 4.69e+03 6.32e+00 bond pdb=" CA PRO B 715 " pdb=" C PRO B 715 " ideal model delta sigma weight residual 1.520 1.552 -0.033 1.42e-02 4.96e+03 5.39e+00 bond pdb=" CD1 TYR A 448 " pdb=" CE1 TYR A 448 " ideal model delta sigma weight residual 1.382 1.321 0.061 3.00e-02 1.11e+03 4.17e+00 bond pdb=" C ASN A 444 " pdb=" N PRO A 445 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.03e+00 bond pdb=" N PRO A 449 " pdb=" CA PRO A 449 " ideal model delta sigma weight residual 1.472 1.494 -0.022 1.32e-02 5.74e+03 2.90e+00 ... (remaining 7892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10402 1.95 - 3.90: 229 3.90 - 5.85: 31 5.85 - 7.80: 6 7.80 - 9.75: 4 Bond angle restraints: 10672 Sorted by residual: angle pdb=" N GLU B 813 " pdb=" CA GLU B 813 " pdb=" C GLU B 813 " ideal model delta sigma weight residual 114.62 107.68 6.94 1.14e+00 7.69e-01 3.71e+01 angle pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " pdb=" CG GLN A 348 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" C ALA B 596 " pdb=" N VAL B 597 " pdb=" CA VAL B 597 " ideal model delta sigma weight residual 121.97 129.51 -7.54 1.80e+00 3.09e-01 1.76e+01 angle pdb=" CA GLU B 813 " pdb=" C GLU B 813 " pdb=" N SER B 814 " ideal model delta sigma weight residual 119.71 115.60 4.11 1.17e+00 7.31e-01 1.23e+01 angle pdb=" CA VAL B 597 " pdb=" CB VAL B 597 " pdb=" CG1 VAL B 597 " ideal model delta sigma weight residual 110.40 115.75 -5.35 1.70e+00 3.46e-01 9.89e+00 ... (remaining 10667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4026 17.92 - 35.83: 608 35.83 - 53.75: 170 53.75 - 71.67: 21 71.67 - 89.59: 13 Dihedral angle restraints: 4838 sinusoidal: 1989 harmonic: 2849 Sorted by residual: dihedral pdb=" CB CYS A 258 " pdb=" SG CYS A 258 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual -86.00 -5.84 -80.16 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 918 " pdb=" SG CYS B 918 " pdb=" SG CYS B 921 " pdb=" CB CYS B 921 " ideal model delta sinusoidal sigma weight residual -86.00 -17.29 -68.71 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CA CYS B 918 " pdb=" C CYS B 918 " pdb=" N TYR B 919 " pdb=" CA TYR B 919 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 4835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1095 0.081 - 0.162: 97 0.162 - 0.244: 3 0.244 - 0.325: 1 0.325 - 0.406: 1 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CB VAL B 597 " pdb=" CA VAL B 597 " pdb=" CG1 VAL B 597 " pdb=" CG2 VAL B 597 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 63 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE B 625 " pdb=" CA ILE B 625 " pdb=" CG1 ILE B 625 " pdb=" CG2 ILE B 625 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1194 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 853 " 0.020 2.00e-02 2.50e+03 1.86e-02 4.35e+00 pdb=" CG ASN B 853 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 853 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 853 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B1102 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 444 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 445 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 83 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 84 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.029 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 794 2.75 - 3.28: 7089 3.28 - 3.82: 11126 3.82 - 4.36: 11629 4.36 - 4.90: 21365 Nonbonded interactions: 52003 Sorted by model distance: nonbonded pdb=" OD2 ASP B 614 " pdb=" OG SER B 902 " model vdw 2.208 3.040 nonbonded pdb=" O SER B 934 " pdb=" OG SER B 934 " model vdw 2.244 3.040 nonbonded pdb=" O ASP B 639 " pdb=" ND2 ASN B 714 " model vdw 2.245 3.120 nonbonded pdb=" NE2 HIS A 243 " pdb=" OH TYR A 328 " model vdw 2.273 3.120 nonbonded pdb=" OG SER A 152 " pdb=" OE1 GLU A 154 " model vdw 2.278 3.040 ... (remaining 51998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 20.810 Find NCS groups from input model: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 0.061 7897 Z= 0.226 Angle : 0.676 9.747 10672 Z= 0.343 Chirality : 0.047 0.406 1197 Planarity : 0.004 0.052 1357 Dihedral : 18.132 89.585 2970 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.12 % Favored : 86.68 % Rotamer: Outliers : 0.23 % Allowed : 35.99 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.25), residues: 1006 helix: 0.21 (0.45), residues: 147 sheet: -1.27 (0.36), residues: 228 loop : -2.74 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 453 HIS 0.005 0.001 HIS B 967 PHE 0.019 0.001 PHE A 330 TYR 0.019 0.002 TYR B 854 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.1923 time to fit residues: 25.1566 Evaluate side-chains 89 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 0.1980 chunk 42 optimal weight: 0.0050 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 582 ASN B 626 ASN ** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7897 Z= 0.176 Angle : 0.650 6.808 10672 Z= 0.327 Chirality : 0.044 0.244 1197 Planarity : 0.004 0.049 1357 Dihedral : 5.552 45.311 1198 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.13 % Favored : 87.57 % Rotamer: Outliers : 0.23 % Allowed : 2.93 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.25), residues: 1006 helix: 0.50 (0.45), residues: 149 sheet: -1.40 (0.35), residues: 230 loop : -2.74 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 480 HIS 0.009 0.001 HIS B 967 PHE 0.027 0.001 PHE B 699 TYR 0.013 0.001 TYR B 919 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7186 (mtp85) cc_final: 0.6905 (mtp85) REVERT: A 136 ASP cc_start: 0.8244 (t0) cc_final: 0.8011 (t0) REVERT: B 691 CYS cc_start: 0.7439 (t) cc_final: 0.7163 (t) REVERT: B 865 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.7998 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.2304 time to fit residues: 36.4385 Evaluate side-chains 92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS ** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7897 Z= 0.360 Angle : 0.764 8.355 10672 Z= 0.394 Chirality : 0.047 0.289 1197 Planarity : 0.005 0.049 1357 Dihedral : 5.843 39.792 1198 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.51 % Favored : 84.10 % Rotamer: Outliers : 0.23 % Allowed : 5.51 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.24), residues: 1006 helix: 0.09 (0.43), residues: 157 sheet: -1.37 (0.37), residues: 222 loop : -3.04 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 480 HIS 0.008 0.001 HIS A 236 PHE 0.024 0.002 PHE A 418 TYR 0.027 0.002 TYR B 764 ARG 0.005 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 807 ILE cc_start: 0.8510 (mm) cc_final: 0.8235 (mt) REVERT: B 895 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7654 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.2052 time to fit residues: 30.6711 Evaluate side-chains 84 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7897 Z= 0.240 Angle : 0.672 7.706 10672 Z= 0.342 Chirality : 0.045 0.271 1197 Planarity : 0.004 0.049 1357 Dihedral : 5.542 38.603 1198 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.32 % Favored : 86.18 % Rotamer: Outliers : 0.23 % Allowed : 4.10 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.24), residues: 1006 helix: 0.12 (0.44), residues: 157 sheet: -1.41 (0.36), residues: 223 loop : -3.02 (0.20), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 480 HIS 0.008 0.001 HIS B 967 PHE 0.012 0.001 PHE B1029 TYR 0.017 0.002 TYR B 919 ARG 0.004 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8520 (ppp) cc_final: 0.8259 (ppp) REVERT: A 186 ILE cc_start: 0.8798 (pt) cc_final: 0.8587 (pt) REVERT: B 651 ARG cc_start: 0.8549 (mtp85) cc_final: 0.7179 (mtt180) REVERT: B 691 CYS cc_start: 0.7427 (t) cc_final: 0.7122 (t) REVERT: B 807 ILE cc_start: 0.8464 (mm) cc_final: 0.8194 (mt) REVERT: B 869 SER cc_start: 0.9235 (t) cc_final: 0.9003 (t) REVERT: B 895 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7639 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.1831 time to fit residues: 29.0140 Evaluate side-chains 94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7897 Z= 0.281 Angle : 0.702 8.878 10672 Z= 0.358 Chirality : 0.046 0.265 1197 Planarity : 0.005 0.046 1357 Dihedral : 5.623 41.656 1198 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.50 % Allowed : 16.50 % Favored : 83.00 % Rotamer: Outliers : 0.23 % Allowed : 3.05 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 1006 helix: 0.18 (0.44), residues: 154 sheet: -1.54 (0.36), residues: 229 loop : -3.07 (0.21), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 480 HIS 0.007 0.001 HIS B 967 PHE 0.015 0.002 PHE A 225 TYR 0.017 0.002 TYR B 764 ARG 0.002 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 186 ILE cc_start: 0.8823 (pt) cc_final: 0.8558 (pt) REVERT: B 691 CYS cc_start: 0.7486 (t) cc_final: 0.7208 (t) REVERT: B 807 ILE cc_start: 0.8523 (mm) cc_final: 0.8222 (mt) REVERT: B 867 GLU cc_start: 0.8368 (tp30) cc_final: 0.8139 (tp30) REVERT: B 869 SER cc_start: 0.9280 (t) cc_final: 0.8964 (t) REVERT: B 895 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7168 (ttm-80) REVERT: B 898 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7170 (ptp-170) outliers start: 2 outliers final: 0 residues processed: 109 average time/residue: 0.1912 time to fit residues: 28.9154 Evaluate side-chains 92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS ** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7897 Z= 0.281 Angle : 0.707 8.605 10672 Z= 0.360 Chirality : 0.046 0.285 1197 Planarity : 0.005 0.071 1357 Dihedral : 5.684 41.696 1198 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.51 % Favored : 84.99 % Rotamer: Outliers : 0.12 % Allowed : 2.46 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.24), residues: 1006 helix: 0.23 (0.43), residues: 160 sheet: -1.62 (0.36), residues: 219 loop : -3.14 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 480 HIS 0.007 0.001 HIS B 967 PHE 0.012 0.002 PHE A 455 TYR 0.017 0.002 TYR B 764 ARG 0.004 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: B 691 CYS cc_start: 0.7530 (t) cc_final: 0.7304 (t) REVERT: B 807 ILE cc_start: 0.8524 (mm) cc_final: 0.8250 (mt) REVERT: B 869 SER cc_start: 0.9305 (t) cc_final: 0.9012 (t) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2002 time to fit residues: 31.5574 Evaluate side-chains 95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 747 HIS B 808 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7897 Z= 0.200 Angle : 0.647 7.305 10672 Z= 0.327 Chirality : 0.044 0.261 1197 Planarity : 0.005 0.057 1357 Dihedral : 5.372 40.117 1198 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.72 % Favored : 85.79 % Rotamer: Outliers : 0.12 % Allowed : 1.64 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.24), residues: 1006 helix: 0.46 (0.44), residues: 157 sheet: -1.72 (0.36), residues: 212 loop : -3.04 (0.20), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 480 HIS 0.007 0.001 HIS B 967 PHE 0.012 0.001 PHE A 225 TYR 0.016 0.002 TYR A 318 ARG 0.003 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: B 807 ILE cc_start: 0.8521 (mm) cc_final: 0.8222 (mt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1888 time to fit residues: 28.1793 Evaluate side-chains 90 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 808 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7897 Z= 0.205 Angle : 0.669 10.684 10672 Z= 0.336 Chirality : 0.044 0.251 1197 Planarity : 0.005 0.056 1357 Dihedral : 5.300 39.820 1198 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 13.12 % Favored : 86.28 % Rotamer: Outliers : 0.12 % Allowed : 1.17 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 1006 helix: 0.45 (0.44), residues: 161 sheet: -1.60 (0.36), residues: 216 loop : -3.03 (0.20), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 480 HIS 0.006 0.001 HIS B 967 PHE 0.010 0.001 PHE A 225 TYR 0.014 0.002 TYR B 919 ARG 0.002 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 691 CYS cc_start: 0.7330 (t) cc_final: 0.7022 (t) REVERT: B 807 ILE cc_start: 0.8489 (mm) cc_final: 0.8220 (mt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1821 time to fit residues: 28.0339 Evaluate side-chains 94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7897 Z= 0.245 Angle : 0.688 9.659 10672 Z= 0.347 Chirality : 0.045 0.278 1197 Planarity : 0.005 0.052 1357 Dihedral : 5.461 40.263 1198 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.60 % Allowed : 14.61 % Favored : 84.79 % Rotamer: Outliers : 0.12 % Allowed : 0.94 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.24), residues: 1006 helix: 0.39 (0.43), residues: 162 sheet: -1.55 (0.36), residues: 211 loop : -3.12 (0.20), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 480 HIS 0.006 0.001 HIS B 967 PHE 0.012 0.001 PHE B1052 TYR 0.021 0.002 TYR A 318 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7290 (mtm110) REVERT: B 691 CYS cc_start: 0.7369 (t) cc_final: 0.7052 (t) REVERT: B 807 ILE cc_start: 0.8485 (mm) cc_final: 0.8228 (mt) REVERT: B 894 TYR cc_start: 0.8945 (p90) cc_final: 0.8668 (p90) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1779 time to fit residues: 27.1717 Evaluate side-chains 89 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.0570 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 808 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7897 Z= 0.181 Angle : 0.657 9.811 10672 Z= 0.328 Chirality : 0.044 0.252 1197 Planarity : 0.005 0.056 1357 Dihedral : 5.132 37.335 1198 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.53 % Favored : 87.87 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.24), residues: 1006 helix: 0.58 (0.44), residues: 161 sheet: -1.51 (0.36), residues: 210 loop : -2.99 (0.20), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 480 HIS 0.006 0.001 HIS B 967 PHE 0.009 0.001 PHE A 225 TYR 0.015 0.001 TYR B 919 ARG 0.002 0.000 ARG B 865 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7278 (mtm110) REVERT: B 691 CYS cc_start: 0.7407 (t) cc_final: 0.7119 (t) REVERT: B 807 ILE cc_start: 0.8484 (mm) cc_final: 0.8223 (mt) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1749 time to fit residues: 28.0993 Evaluate side-chains 93 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.206655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.150525 restraints weight = 87007.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.153193 restraints weight = 50818.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.144582 restraints weight = 41511.729| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7897 Z= 0.194 Angle : 0.663 9.297 10672 Z= 0.331 Chirality : 0.045 0.252 1197 Planarity : 0.005 0.052 1357 Dihedral : 5.118 37.801 1198 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.60 % Allowed : 12.92 % Favored : 86.48 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.24), residues: 1006 helix: 0.57 (0.44), residues: 160 sheet: -1.49 (0.36), residues: 214 loop : -2.97 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 480 HIS 0.005 0.001 HIS B 967 PHE 0.015 0.001 PHE A 418 TYR 0.025 0.002 TYR A 318 ARG 0.002 0.000 ARG B 865 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.90 seconds wall clock time: 31 minutes 56.92 seconds (1916.92 seconds total)