Starting phenix.real_space_refine on Tue Sep 24 16:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/09_2024/6xms_22262.cif" } resolution = 3.4 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= 0.001 sd= 0.043 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 38 5.16 5 C 5434 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8383 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 1042} Chain breaks: 3 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 136 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.61, per 1000 atoms: 0.67 Number of scatterers: 8389 At special positions: 0 Unit cell: (82.8, 95.4, 135.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1537 8.00 N 1374 7.00 C 5434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 48.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.579A pdb=" N LYS A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 156 through 163 removed outlier: 3.957A pdb=" N PHE A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 188 through 197 removed outlier: 4.073A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 217 through 247 removed outlier: 3.765A pdb=" N SER A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.437A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 4.012A pdb=" N GLU A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 387 removed outlier: 3.643A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 424 removed outlier: 4.002A pdb=" N TYR A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 4.234A pdb=" N VAL A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.855A pdb=" N MET A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.586A pdb=" N ARG A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.647A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 471 through 479' Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.561A pdb=" N ILE A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.721A pdb=" N GLU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.862A pdb=" N TYR A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 removed outlier: 4.336A pdb=" N VAL A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 753 through 762 removed outlier: 4.633A pdb=" N ASP A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 773 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 793 through 807 removed outlier: 3.563A pdb=" N LYS A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.593A pdb=" N ASP A 957 " --> pdb=" O LYS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1012 removed outlier: 4.526A pdb=" N ALA A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.925A pdb=" N CYS A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1084 Processing helix chain 'A' and resid 1099 through 1120 removed outlier: 3.669A pdb=" N THR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.508A pdb=" N TYR A1137 " --> pdb=" O ASN A1133 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1168 through 1198 removed outlier: 4.180A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 3.664A pdb=" N VAL A 143 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 138 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.723A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.868A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.549A pdb=" N LEU A 267 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 366 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.532A pdb=" N SER A 299 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 745 removed outlier: 3.543A pdb=" N PHE A 745 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 719 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR A 766 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 721 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 765 " --> pdb=" O ALA A 790 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N TYR A 789 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 515 through 516 removed outlier: 3.503A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 502 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 668 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 668 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 636 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 670 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG A 634 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 605 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 641 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 578 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.640A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1158 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: 3.17 Time building geometry restraints manager: 2.61 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: 2661 1.34 - 1.46: 1456 1.46 - 1.57: 4384 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8568 Sorted by residual: bond pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.685 1.779 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" F3 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.685 1.779 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" F4 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.686 1.780 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CA TYR A 567 " pdb=" CB TYR A 567 " ideal model delta sigma weight residual 1.539 1.521 0.018 1.36e-02 5.41e+03 1.74e+00 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.03: 11629 14.03 - 28.06: 4 28.06 - 42.10: 0 42.10 - 56.13: 0 56.13 - 70.16: 2 Bond angle restraints: 11635 Sorted by residual: angle pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " pdb=" F2 ALF A1302 " ideal model delta sigma weight residual 108.68 178.84 -70.16 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1302 " pdb="AL ALF A1302 " pdb=" F4 ALF A1302 " ideal model delta sigma weight residual 109.63 178.62 -68.99 3.00e+00 1.11e-01 5.29e+02 angle pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " pdb=" F4 ALF A1302 " ideal model delta sigma weight residual 110.21 89.59 20.62 3.00e+00 1.11e-01 4.72e+01 angle pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " pdb=" F3 ALF A1302 " ideal model delta sigma weight residual 109.59 89.66 19.93 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " pdb=" F3 ALF A1302 " ideal model delta sigma weight residual 109.69 90.17 19.52 3.00e+00 1.11e-01 4.23e+01 ... (remaining 11630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4596 15.91 - 31.81: 426 31.81 - 47.72: 82 47.72 - 63.63: 10 63.63 - 79.54: 3 Dihedral angle restraints: 5117 sinusoidal: 1948 harmonic: 3169 Sorted by residual: dihedral pdb=" CA ARG A 760 " pdb=" C ARG A 760 " pdb=" N TYR A 761 " pdb=" CA TYR A 761 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP A 762 " pdb=" C ASP A 762 " pdb=" N ILE A 763 " pdb=" CA ILE A 763 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA VAL A 737 " pdb=" C VAL A 737 " pdb=" N GLU A 738 " pdb=" CA GLU A 738 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 773 0.031 - 0.063: 407 0.063 - 0.094: 125 0.094 - 0.126: 52 0.126 - 0.157: 8 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA TYR A 761 " pdb=" N TYR A 761 " pdb=" C TYR A 761 " pdb=" CB TYR A 761 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE A 368 " pdb=" N ILE A 368 " pdb=" C ILE A 368 " pdb=" CB ILE A 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE A 743 " pdb=" N ILE A 743 " pdb=" C ILE A 743 " pdb=" CB ILE A 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1362 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 75 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 274 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1039 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A1040 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1040 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1040 " 0.020 5.00e-02 4.00e+02 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 32 2.47 - 3.08: 5776 3.08 - 3.68: 11489 3.68 - 4.29: 16285 4.29 - 4.90: 28062 Nonbonded interactions: 61644 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" F1 ALF A1302 " model vdw 1.862 2.120 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1301 " model vdw 2.019 2.170 nonbonded pdb=" OD2 ASP A 746 " pdb=" OG SER A 748 " model vdw 2.150 3.040 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1301 " model vdw 2.165 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 ALF A1302 " model vdw 2.200 2.990 ... (remaining 61639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.020 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.670 Find NCS groups from input model: 0.090 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8568 Z= 0.415 Angle : 1.183 70.161 11635 Z= 0.489 Chirality : 0.043 0.157 1365 Planarity : 0.004 0.046 1467 Dihedral : 12.682 79.535 3065 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % 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: -2.39 (0.22), residues: 1083 helix: -0.40 (0.22), residues: 468 sheet: -2.87 (0.39), residues: 134 loop : -2.38 (0.23), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.022 0.002 PHE A1032 TYR 0.015 0.002 TYR A 625 ARG 0.004 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2026 time to fit residues: 13.5673 Evaluate side-chains 34 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 533 HIS ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 HIS A 785 HIS A 987 ASN A1089 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8568 Z= 0.180 Angle : 0.529 11.125 11635 Z= 0.275 Chirality : 0.040 0.162 1365 Planarity : 0.004 0.038 1467 Dihedral : 4.271 20.363 1152 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 8.58 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1083 helix: 1.11 (0.24), residues: 484 sheet: -2.29 (0.42), residues: 129 loop : -1.90 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS A 706 PHE 0.015 0.001 PHE A 402 TYR 0.012 0.001 TYR A 625 ARG 0.002 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.000 Fit side-chains REVERT: A 1198 MET cc_start: 0.8897 (tpt) cc_final: 0.8607 (tpt) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.1777 time to fit residues: 12.5235 Evaluate side-chains 37 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8568 Z= 0.159 Angle : 0.485 12.220 11635 Z= 0.250 Chirality : 0.039 0.143 1365 Planarity : 0.003 0.034 1467 Dihedral : 3.978 19.934 1152 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.23 % Allowed : 9.70 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1083 helix: 1.81 (0.25), residues: 484 sheet: -2.12 (0.44), residues: 123 loop : -1.58 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.009 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.005 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.009 Fit side-chains REVERT: A 497 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8678 (pp) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.1798 time to fit residues: 13.9951 Evaluate side-chains 43 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8568 Z= 0.180 Angle : 0.488 12.810 11635 Z= 0.249 Chirality : 0.039 0.140 1365 Planarity : 0.003 0.033 1467 Dihedral : 3.903 19.977 1152 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.11 % Allowed : 11.93 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1083 helix: 2.12 (0.25), residues: 484 sheet: -1.98 (0.44), residues: 123 loop : -1.40 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.010 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.003 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 1.021 Fit side-chains REVERT: A 497 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8682 (pp) REVERT: A 813 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7473 (ttt) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.1797 time to fit residues: 12.7421 Evaluate side-chains 45 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8568 Z= 0.151 Angle : 0.473 13.482 11635 Z= 0.240 Chirality : 0.039 0.142 1365 Planarity : 0.003 0.034 1467 Dihedral : 3.794 19.395 1152 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.00 % Allowed : 14.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1083 helix: 2.25 (0.25), residues: 488 sheet: -1.79 (0.45), residues: 118 loop : -1.35 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.003 0.001 HIS A1069 PHE 0.008 0.001 PHE A 734 TYR 0.010 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.930 Fit side-chains REVERT: A 497 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (pp) REVERT: A 813 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7425 (ttt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1768 time to fit residues: 13.3159 Evaluate side-chains 45 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8568 Z= 0.205 Angle : 0.491 13.768 11635 Z= 0.250 Chirality : 0.039 0.137 1365 Planarity : 0.003 0.034 1467 Dihedral : 3.811 19.933 1152 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.45 % Allowed : 14.60 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1083 helix: 2.30 (0.25), residues: 487 sheet: -1.83 (0.44), residues: 123 loop : -1.27 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.010 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.003 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 1.026 Fit side-chains REVERT: A 497 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 813 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7483 (ttt) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.1742 time to fit residues: 13.5382 Evaluate side-chains 48 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0170 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN A1159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8568 Z= 0.137 Angle : 0.471 14.372 11635 Z= 0.237 Chirality : 0.038 0.136 1365 Planarity : 0.003 0.037 1467 Dihedral : 3.665 19.256 1152 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 15.72 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1083 helix: 2.40 (0.25), residues: 490 sheet: -1.66 (0.45), residues: 123 loop : -1.18 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.002 0.001 HIS A1069 PHE 0.008 0.001 PHE A 128 TYR 0.009 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 1.055 Fit side-chains REVERT: A 813 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7426 (ttt) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.1769 time to fit residues: 12.9801 Evaluate side-chains 43 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8568 Z= 0.200 Angle : 0.492 14.397 11635 Z= 0.249 Chirality : 0.039 0.133 1365 Planarity : 0.003 0.031 1467 Dihedral : 3.736 19.652 1152 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.00 % Allowed : 15.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.26), residues: 1083 helix: 2.47 (0.25), residues: 487 sheet: -1.62 (0.44), residues: 123 loop : -1.17 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.009 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 1.035 Fit side-chains REVERT: A 813 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7437 (ttt) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1818 time to fit residues: 12.7112 Evaluate side-chains 44 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8568 Z= 0.154 Angle : 0.479 14.773 11635 Z= 0.240 Chirality : 0.039 0.130 1365 Planarity : 0.003 0.030 1467 Dihedral : 3.683 19.365 1152 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.11 % Allowed : 15.61 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1083 helix: 2.54 (0.25), residues: 487 sheet: -1.51 (0.45), residues: 123 loop : -1.15 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.008 0.001 PHE A 734 TYR 0.010 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.972 Fit side-chains REVERT: A 813 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7445 (ttt) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.1712 time to fit residues: 13.1693 Evaluate side-chains 45 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8568 Z= 0.194 Angle : 0.494 14.803 11635 Z= 0.248 Chirality : 0.039 0.161 1365 Planarity : 0.003 0.029 1467 Dihedral : 3.729 19.528 1152 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.11 % Allowed : 15.50 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1083 helix: 2.55 (0.24), residues: 487 sheet: -1.49 (0.45), residues: 123 loop : -1.15 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.009 0.001 PHE A 734 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.905 Fit side-chains REVERT: A 813 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7396 (ttt) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.1656 time to fit residues: 11.7548 Evaluate side-chains 45 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.059434 restraints weight = 23302.581| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.99 r_work: 0.2798 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 8568 Z= 0.259 Angle : 0.529 14.565 11635 Z= 0.267 Chirality : 0.040 0.151 1365 Planarity : 0.003 0.029 1467 Dihedral : 3.904 20.453 1152 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.11 % Allowed : 15.72 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.26), residues: 1083 helix: 2.47 (0.24), residues: 487 sheet: -1.50 (0.45), residues: 123 loop : -1.21 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.011 0.001 PHE A 734 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.26 seconds wall clock time: 31 minutes 16.11 seconds (1876.11 seconds total)