Starting phenix.real_space_refine on Tue Mar 3 20:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_22262.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_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/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_22262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_22262.map" model { file = "/net/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_22262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xms_22262/03_2026/6xms_22262.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'GLU:plan': 11, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1} 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: 2.15, per 1000 atoms: 0.26 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: 0.67 Conformation dependent library (CDL) restraints added in 321.7 milliseconds 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: 0.33 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: 1.66 Time building geometry restraints manager: 0.91 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- 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= 0.260 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG A 175 TYR 0.015 0.002 TYR A 625 PHE 0.022 0.002 PHE A1032 TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 8568) covalent geometry : angle 1.18347 (11635) hydrogen bonds : bond 0.17395 ( 399) hydrogen bonds : angle 6.14517 ( 1158) *********************** 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 to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0841 time to fit residues: 5.6955 Evaluate side-chains 34 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062097 restraints weight = 24248.411| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.02 r_work: 0.2887 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8568 Z= 0.137 Angle : 0.536 11.313 11635 Z= 0.279 Chirality : 0.040 0.166 1365 Planarity : 0.004 0.038 1467 Dihedral : 4.321 20.559 1152 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.56 % Allowed : 9.03 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1083 helix: 1.10 (0.24), residues: 483 sheet: -2.31 (0.41), residues: 129 loop : -1.91 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.013 0.001 TYR A 625 PHE 0.015 0.001 PHE A 402 TRP 0.009 0.001 TRP A 415 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8568) covalent geometry : angle 0.53649 (11635) hydrogen bonds : bond 0.05831 ( 399) hydrogen bonds : angle 4.44472 ( 1158) *********************** 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 45 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.330 Fit side-chains REVERT: A 1198 MET cc_start: 0.9088 (tpt) cc_final: 0.8737 (tpt) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.0799 time to fit residues: 5.3054 Evaluate side-chains 37 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 1030 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.075750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.062386 restraints weight = 23717.914| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.95 r_work: 0.2900 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1435 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= 0.128 Angle : 0.504 11.958 11635 Z= 0.261 Chirality : 0.040 0.150 1365 Planarity : 0.003 0.034 1467 Dihedral : 4.089 20.551 1152 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.23 % Allowed : 10.70 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1083 helix: 1.74 (0.24), residues: 484 sheet: -2.18 (0.44), residues: 123 loop : -1.59 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.012 0.001 TYR A 625 PHE 0.011 0.001 PHE A 402 TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8568) covalent geometry : angle 0.50429 (11635) hydrogen bonds : bond 0.05191 ( 399) hydrogen bonds : angle 4.05859 ( 1158) *********************** 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 47 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.351 Fit side-chains REVERT: A 497 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8912 (pp) REVERT: A 654 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (pp) REVERT: A 1198 MET cc_start: 0.9002 (tpt) cc_final: 0.8723 (tpt) outliers start: 11 outliers final: 5 residues processed: 45 average time/residue: 0.0806 time to fit residues: 5.6490 Evaluate side-chains 41 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 654 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.061159 restraints weight = 24717.758| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.03 r_work: 0.2862 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8568 Z= 0.183 Angle : 0.539 12.604 11635 Z= 0.278 Chirality : 0.041 0.157 1365 Planarity : 0.004 0.033 1467 Dihedral : 4.154 21.195 1152 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.34 % Allowed : 13.38 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1083 helix: 1.93 (0.24), residues: 484 sheet: -2.19 (0.43), residues: 123 loop : -1.44 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.014 0.001 TYR A 625 PHE 0.013 0.001 PHE A 402 TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8568) covalent geometry : angle 0.53935 (11635) hydrogen bonds : bond 0.05653 ( 399) hydrogen bonds : angle 4.07281 ( 1158) *********************** 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 to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.329 Fit side-chains REVERT: A 497 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8930 (pp) REVERT: A 654 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7692 (pp) REVERT: A 813 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8185 (ttt) REVERT: A 1198 MET cc_start: 0.9065 (tpt) cc_final: 0.8788 (tpt) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.0703 time to fit residues: 5.0112 Evaluate side-chains 44 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 654 LEU 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 90 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 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 = 0.3225 r_free = 0.3225 target = 0.073206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.059565 restraints weight = 23929.391| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.88 r_work: 0.2797 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8568 Z= 0.164 Angle : 0.523 13.185 11635 Z= 0.269 Chirality : 0.040 0.157 1365 Planarity : 0.003 0.035 1467 Dihedral : 4.113 21.202 1152 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 14.49 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1083 helix: 2.08 (0.25), residues: 484 sheet: -2.17 (0.42), residues: 128 loop : -1.32 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.013 0.001 TYR A 625 PHE 0.012 0.001 PHE A 734 TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8568) covalent geometry : angle 0.52308 (11635) hydrogen bonds : bond 0.05451 ( 399) hydrogen bonds : angle 3.98850 ( 1158) *********************** 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 51 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.273 Fit side-chains REVERT: A 497 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8912 (pp) REVERT: A 543 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 654 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7764 (pp) REVERT: A 813 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8019 (ttt) REVERT: A 1198 MET cc_start: 0.8961 (tpt) cc_final: 0.8725 (tpt) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 0.0750 time to fit residues: 5.8494 Evaluate side-chains 45 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 543 ILE Chi-restraints excluded: chain A residue 654 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.0570 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063245 restraints weight = 23166.675| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.88 r_work: 0.2882 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8568 Z= 0.091 Angle : 0.467 14.019 11635 Z= 0.238 Chirality : 0.038 0.135 1365 Planarity : 0.003 0.037 1467 Dihedral : 3.747 19.416 1152 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.78 % Allowed : 16.39 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1083 helix: 2.41 (0.25), residues: 483 sheet: -1.82 (0.44), residues: 123 loop : -1.34 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.010 0.001 TYR A 625 PHE 0.009 0.001 PHE A 128 TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A1069 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8568) covalent geometry : angle 0.46706 (11635) hydrogen bonds : bond 0.03909 ( 399) hydrogen bonds : angle 3.65233 ( 1158) *********************** 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 47 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.314 Fit side-chains REVERT: A 654 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 813 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7947 (ttt) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.0792 time to fit residues: 5.7134 Evaluate side-chains 43 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.061736 restraints weight = 23534.170| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.88 r_work: 0.2848 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2049 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= 0.118 Angle : 0.485 14.212 11635 Z= 0.245 Chirality : 0.039 0.131 1365 Planarity : 0.003 0.037 1467 Dihedral : 3.741 19.978 1152 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.11 % Allowed : 16.28 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1083 helix: 2.42 (0.25), residues: 487 sheet: -1.77 (0.44), residues: 123 loop : -1.27 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.011 0.001 TYR A 625 PHE 0.011 0.001 PHE A 405 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A1069 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8568) covalent geometry : angle 0.48499 (11635) hydrogen bonds : bond 0.04394 ( 399) hydrogen bonds : angle 3.66269 ( 1158) *********************** 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 49 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.326 Fit side-chains REVERT: A 497 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8904 (pp) REVERT: A 654 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (pp) REVERT: A 813 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7971 (ttt) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.0766 time to fit residues: 5.7541 Evaluate side-chains 47 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 622 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.074256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060487 restraints weight = 23463.629| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.88 r_work: 0.2824 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1989 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= 0.141 Angle : 0.502 14.230 11635 Z= 0.254 Chirality : 0.039 0.139 1365 Planarity : 0.003 0.036 1467 Dihedral : 3.830 20.496 1152 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.34 % Allowed : 16.28 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1083 helix: 2.42 (0.25), residues: 487 sheet: -1.69 (0.45), residues: 123 loop : -1.25 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.012 0.001 TYR A 625 PHE 0.012 0.001 PHE A 405 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8568) covalent geometry : angle 0.50164 (11635) hydrogen bonds : bond 0.04866 ( 399) hydrogen bonds : angle 3.73356 ( 1158) *********************** 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 49 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.379 Fit side-chains REVERT: A 497 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8892 (pp) REVERT: A 654 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 813 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8065 (ttt) outliers start: 12 outliers final: 7 residues processed: 48 average time/residue: 0.0754 time to fit residues: 5.7597 Evaluate side-chains 46 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 622 ASP Chi-restraints excluded: chain A residue 654 LEU 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 15 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.073620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.059844 restraints weight = 23527.690| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.87 r_work: 0.2810 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8568 Z= 0.160 Angle : 0.528 14.416 11635 Z= 0.266 Chirality : 0.040 0.155 1365 Planarity : 0.003 0.036 1467 Dihedral : 3.916 20.822 1152 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.11 % Allowed : 16.72 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1083 helix: 2.37 (0.24), residues: 487 sheet: -1.68 (0.45), residues: 123 loop : -1.27 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.012 0.001 TYR A 625 PHE 0.012 0.001 PHE A 405 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8568) covalent geometry : angle 0.52759 (11635) hydrogen bonds : bond 0.05148 ( 399) hydrogen bonds : angle 3.79472 ( 1158) *********************** 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 46 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.334 Fit side-chains REVERT: A 497 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8886 (pp) REVERT: A 654 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7848 (pp) REVERT: A 813 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8051 (ttt) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.0785 time to fit residues: 5.5851 Evaluate side-chains 45 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 622 ASP Chi-restraints excluded: chain A residue 654 LEU 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 29 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061564 restraints weight = 23393.999| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.88 r_work: 0.2838 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8568 Z= 0.112 Angle : 0.490 14.872 11635 Z= 0.246 Chirality : 0.039 0.150 1365 Planarity : 0.003 0.036 1467 Dihedral : 3.802 20.433 1152 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.11 % Allowed : 16.83 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1083 helix: 2.45 (0.24), residues: 489 sheet: -1.59 (0.45), residues: 123 loop : -1.27 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.010 0.001 TYR A 625 PHE 0.011 0.001 PHE A 405 TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8568) covalent geometry : angle 0.49044 (11635) hydrogen bonds : bond 0.04506 ( 399) hydrogen bonds : angle 3.66465 ( 1158) ********************** 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 47 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: A 497 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8869 (pp) REVERT: A 654 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 813 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7974 (ttt) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.0720 time to fit residues: 5.1584 Evaluate side-chains 47 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 622 ASP Chi-restraints excluded: chain A residue 654 LEU 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 62 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061248 restraints weight = 23197.452| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.98 r_work: 0.2846 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2229 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= 0.109 Angle : 0.479 13.098 11635 Z= 0.241 Chirality : 0.039 0.148 1365 Planarity : 0.003 0.036 1467 Dihedral : 3.723 19.960 1152 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.23 % Allowed : 16.83 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1083 helix: 2.52 (0.24), residues: 488 sheet: -1.51 (0.46), residues: 123 loop : -1.26 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 588 TYR 0.010 0.001 TYR A 625 PHE 0.010 0.001 PHE A 405 TRP 0.007 0.001 TRP A 415 HIS 0.003 0.001 HIS A1069 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8568) covalent geometry : angle 0.47897 (11635) hydrogen bonds : bond 0.04351 ( 399) hydrogen bonds : angle 3.62496 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.99 seconds wall clock time: 28 minutes 28.92 seconds (1708.92 seconds total)