Starting phenix.real_space_refine on Wed Feb 4 07:31:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.map" model { file = "/net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o2z_70053/02_2026/9o2z_70053.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Zn 2 6.06 5 P 2 5.49 5 S 57 5.16 5 C 5802 2.51 5 N 1576 2.21 5 O 1701 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9141 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3311 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2291 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1738 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1766 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'CHU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 673 SG CYS A 248 51.730 46.621 83.670 1.00117.18 S ATOM 698 SG CYS A 251 54.310 44.897 83.822 1.00131.48 S ATOM 880 SG CYS A 272 54.447 48.603 85.273 1.00155.91 S ATOM 786 SG CYS A 261 42.548 57.390 83.340 1.00125.35 S ATOM 808 SG CYS A 264 43.082 55.784 81.204 1.00125.37 S Time building chain proxies: 2.37, per 1000 atoms: 0.26 Number of scatterers: 9141 At special positions: 0 Unit cell: (76.14, 93.96, 127.17, 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) Zn 2 29.99 S 57 16.00 P 2 15.00 F 1 9.00 O 1701 8.00 N 1576 7.00 C 5802 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: 0.83 Conformation dependent library (CDL) restraints added in 357.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 235 " 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 58.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.025A pdb=" N SER A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.027A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.503A pdb=" N HIS A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 removed outlier: 3.509A pdb=" N ASP A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 635 through 638 removed outlier: 3.550A pdb=" N ASP A 638 " --> pdb=" O PHE A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.521A pdb=" N VAL A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 677 through 681 removed outlier: 3.861A pdb=" N LYS A 680 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 681 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 681' Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 694 through 698 removed outlier: 3.664A pdb=" N LYS A 698 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.860A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.548A pdb=" N GLU B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 162 through 185 removed outlier: 3.788A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.870A pdb=" N ASP B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 240 through 259 removed outlier: 3.632A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 4.046A pdb=" N LEU B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 removed outlier: 4.115A pdb=" N LYS B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.700A pdb=" N LYS B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.771A pdb=" N LEU B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 380 " --> pdb=" O CYS B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.928A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.602A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 69 removed outlier: 3.926A pdb=" N TYR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 105 removed outlier: 4.138A pdb=" N MET C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 111 through 133 removed outlier: 4.001A pdb=" N VAL C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 160 removed outlier: 3.932A pdb=" N LYS C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 removed outlier: 3.650A pdb=" N LEU C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.741A pdb=" N THR C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 230 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.077A pdb=" N GLN D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.980A pdb=" N MET D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 68 removed outlier: 3.643A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 104 removed outlier: 3.932A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 Processing helix chain 'D' and resid 138 through 157 removed outlier: 3.726A pdb=" N VAL D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 203 Processing helix chain 'D' and resid 207 through 230 removed outlier: 4.477A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.776A pdb=" N HIS A 223 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 241 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 475 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 76 removed outlier: 7.453A pdb=" N LYS B 84 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU B 73 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL B 82 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 81 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 98 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B 135 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 140 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 133 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 142 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 469 hydrogen bonds defined for protein. 1356 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: 1.40 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1726 1.33 - 1.45: 2202 1.45 - 1.57: 5279 1.57 - 1.69: 10 1.69 - 1.81: 90 Bond restraints: 9307 Sorted by residual: bond pdb=" N ILE A 452 " pdb=" CA ILE A 452 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.56e+00 bond pdb=" N ASP A 449 " pdb=" CA ASP A 449 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.03e+00 bond pdb=" N TRP A 450 " pdb=" CA TRP A 450 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.16e-02 7.43e+03 5.86e+00 bond pdb=" N ASP A 448 " pdb=" CA ASP A 448 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.21e-02 6.83e+03 5.52e+00 bond pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.28e-02 6.10e+03 3.82e+00 ... (remaining 9302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 12422 3.21 - 6.42: 108 6.42 - 9.62: 12 9.62 - 12.83: 4 12.83 - 16.04: 2 Bond angle restraints: 12548 Sorted by residual: angle pdb=" C HIS A 370 " pdb=" CA HIS A 370 " pdb=" CB HIS A 370 " ideal model delta sigma weight residual 110.10 94.06 16.04 1.90e+00 2.77e-01 7.13e+01 angle pdb=" CA LEU D 98 " pdb=" CB LEU D 98 " pdb=" CG LEU D 98 " ideal model delta sigma weight residual 116.30 130.10 -13.80 3.50e+00 8.16e-02 1.56e+01 angle pdb=" N ASP A 448 " pdb=" CA ASP A 448 " pdb=" C ASP A 448 " ideal model delta sigma weight residual 111.28 107.06 4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N PHE A 250 " pdb=" CA PHE A 250 " pdb=" C PHE A 250 " ideal model delta sigma weight residual 113.43 108.60 4.83 1.26e+00 6.30e-01 1.47e+01 angle pdb=" N GLU D 81 " pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " ideal model delta sigma weight residual 110.12 115.42 -5.30 1.47e+00 4.63e-01 1.30e+01 ... (remaining 12543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4818 17.85 - 35.69: 670 35.69 - 53.54: 162 53.54 - 71.39: 15 71.39 - 89.24: 11 Dihedral angle restraints: 5676 sinusoidal: 2323 harmonic: 3353 Sorted by residual: dihedral pdb=" C HIS A 370 " pdb=" N HIS A 370 " pdb=" CA HIS A 370 " pdb=" CB HIS A 370 " ideal model delta harmonic sigma weight residual -122.60 -105.63 -16.97 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" CA LYS D 158 " pdb=" C LYS D 158 " pdb=" N GLU D 159 " pdb=" CA GLU D 159 " ideal model delta harmonic sigma weight residual 180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE B 263 " pdb=" C ILE B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1015 0.047 - 0.094: 297 0.094 - 0.140: 64 0.140 - 0.187: 6 0.187 - 0.234: 6 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA HIS A 370 " pdb=" N HIS A 370 " pdb=" C HIS A 370 " pdb=" CB HIS A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU C 43 " pdb=" CB LEU C 43 " pdb=" CD1 LEU C 43 " pdb=" CD2 LEU C 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR D 194 " pdb=" CA THR D 194 " pdb=" OG1 THR D 194 " pdb=" CG2 THR D 194 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1385 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 228 " -0.030 2.00e-02 2.50e+03 1.95e-02 9.54e+00 pdb=" CG TRP C 228 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 228 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 228 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 228 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 228 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 228 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 228 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 228 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 228 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 126 " -0.018 2.00e-02 2.50e+03 1.80e-02 6.49e+00 pdb=" CG TYR D 126 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR D 126 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 126 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 126 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 126 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 126 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 178 " -0.017 2.00e-02 2.50e+03 1.75e-02 6.11e+00 pdb=" CG TYR D 178 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 178 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 178 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 178 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 178 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 178 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 178 " 0.001 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 39 2.37 - 3.00: 5278 3.00 - 3.64: 14680 3.64 - 4.27: 20933 4.27 - 4.90: 33551 Nonbonded interactions: 74481 Sorted by model distance: nonbonded pdb=" O HIS A 370 " pdb=" ND1 HIS A 370 " model vdw 1.740 3.120 nonbonded pdb=" OG SER C 37 " pdb=" OE1 GLU C 40 " model vdw 2.073 3.040 nonbonded pdb=" OE1 GLN D 161 " pdb=" OG1 THR D 163 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP D 124 " pdb=" NH2 ARG D 127 " model vdw 2.180 3.120 nonbonded pdb=" OD1 ASP C 124 " pdb=" NH2 ARG C 127 " model vdw 2.183 3.120 ... (remaining 74476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 104 through \ 133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE )) or resid 159 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 229 or (resid 230 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'D' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB \ or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 159 through 203 or resid 210 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.005 0.285 9313 Z= 0.207 Angle : 0.840 16.041 12548 Z= 0.460 Chirality : 0.047 0.234 1388 Planarity : 0.004 0.037 1602 Dihedral : 17.105 89.236 3500 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.24 % Allowed : 27.04 % Favored : 70.71 % Cbeta Deviations : 0.09 % 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: -1.69 (0.24), residues: 1117 helix: -0.38 (0.21), residues: 583 sheet: -2.03 (0.55), residues: 77 loop : -1.86 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 113 TYR 0.044 0.002 TYR D 126 PHE 0.026 0.002 PHE B 223 TRP 0.052 0.002 TRP C 228 HIS 0.006 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9307) covalent geometry : angle 0.83972 (12548) hydrogen bonds : bond 0.17896 ( 469) hydrogen bonds : angle 7.47937 ( 1356) metal coordination : bond 0.11617 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8024 (mmm160) REVERT: A 254 LEU cc_start: 0.7579 (tp) cc_final: 0.7197 (tp) REVERT: A 550 MET cc_start: 0.7444 (mmt) cc_final: 0.7170 (mtp) REVERT: A 738 PHE cc_start: 0.2399 (m-80) cc_final: 0.0389 (t80) REVERT: B 249 MET cc_start: 0.8020 (ppp) cc_final: 0.7780 (ppp) REVERT: B 256 MET cc_start: 0.6745 (mmm) cc_final: 0.5717 (mpp) REVERT: B 356 MET cc_start: 0.4005 (mpp) cc_final: 0.3636 (mpp) REVERT: C 83 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (ttt-90) REVERT: D 89 GLU cc_start: 0.8605 (tt0) cc_final: 0.8052 (pt0) REVERT: D 90 LEU cc_start: 0.9338 (pp) cc_final: 0.8760 (tp) outliers start: 22 outliers final: 17 residues processed: 186 average time/residue: 0.0823 time to fit residues: 22.1006 Evaluate side-chains 175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.131423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100041 restraints weight = 25066.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102938 restraints weight = 15460.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.105151 restraints weight = 11078.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.106755 restraints weight = 8783.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107265 restraints weight = 7396.979| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9313 Z= 0.204 Angle : 0.693 7.703 12548 Z= 0.365 Chirality : 0.044 0.169 1388 Planarity : 0.005 0.038 1602 Dihedral : 7.511 94.374 1297 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.69 % Allowed : 21.22 % Favored : 74.08 % 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: -1.33 (0.25), residues: 1117 helix: -0.12 (0.21), residues: 581 sheet: -1.76 (0.57), residues: 73 loop : -1.65 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 662 TYR 0.031 0.002 TYR D 178 PHE 0.023 0.002 PHE C 174 TRP 0.030 0.002 TRP C 228 HIS 0.005 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9307) covalent geometry : angle 0.69309 (12548) hydrogen bonds : bond 0.04579 ( 469) hydrogen bonds : angle 5.69930 ( 1356) metal coordination : bond 0.00410 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8542 (tptp) cc_final: 0.8084 (mttt) REVERT: A 260 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5997 (tpt-90) REVERT: A 507 LYS cc_start: 0.8331 (tppt) cc_final: 0.8106 (tppt) REVERT: A 733 LEU cc_start: 0.8251 (mm) cc_final: 0.7901 (tp) REVERT: A 738 PHE cc_start: 0.2417 (m-80) cc_final: 0.0206 (t80) REVERT: C 78 MET cc_start: 0.8121 (mtt) cc_final: 0.7876 (mtt) REVERT: C 83 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7777 (ttt-90) REVERT: C 99 SER cc_start: 0.9017 (m) cc_final: 0.8784 (t) REVERT: D 89 GLU cc_start: 0.8531 (tt0) cc_final: 0.8006 (pt0) REVERT: D 90 LEU cc_start: 0.9304 (pp) cc_final: 0.8655 (tp) REVERT: D 219 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8498 (mm110) outliers start: 46 outliers final: 23 residues processed: 207 average time/residue: 0.0760 time to fit residues: 23.2580 Evaluate side-chains 180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 224 ASN ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101991 restraints weight = 24624.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.105099 restraints weight = 14386.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.107445 restraints weight = 10073.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.108637 restraints weight = 7827.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.109756 restraints weight = 6654.969| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9313 Z= 0.149 Angle : 0.639 9.823 12548 Z= 0.330 Chirality : 0.043 0.164 1388 Planarity : 0.004 0.064 1602 Dihedral : 6.878 88.456 1281 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.37 % Allowed : 22.65 % Favored : 73.98 % 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: -1.03 (0.25), residues: 1117 helix: 0.19 (0.21), residues: 586 sheet: -1.71 (0.62), residues: 64 loop : -1.63 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 662 TYR 0.020 0.002 TYR D 178 PHE 0.019 0.001 PHE C 174 TRP 0.018 0.002 TRP C 228 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9307) covalent geometry : angle 0.63920 (12548) hydrogen bonds : bond 0.04153 ( 469) hydrogen bonds : angle 5.34800 ( 1356) metal coordination : bond 0.00286 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8446 (tptp) cc_final: 0.8080 (mttt) REVERT: A 507 LYS cc_start: 0.8334 (tppt) cc_final: 0.8072 (tppt) REVERT: A 550 MET cc_start: 0.7642 (mmt) cc_final: 0.7120 (mmt) REVERT: A 733 LEU cc_start: 0.8209 (mm) cc_final: 0.7850 (tp) REVERT: A 738 PHE cc_start: 0.2329 (m-80) cc_final: 0.0146 (t80) REVERT: B 256 MET cc_start: 0.7836 (mpp) cc_final: 0.6585 (mpp) REVERT: C 99 SER cc_start: 0.8964 (m) cc_final: 0.8711 (t) REVERT: C 154 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8619 (mm-30) REVERT: D 89 GLU cc_start: 0.8453 (tt0) cc_final: 0.8110 (pt0) REVERT: D 90 LEU cc_start: 0.9307 (pp) cc_final: 0.8692 (tp) REVERT: D 118 TYR cc_start: 0.8736 (m-80) cc_final: 0.8509 (m-80) REVERT: D 219 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8592 (mm110) outliers start: 33 outliers final: 22 residues processed: 195 average time/residue: 0.0646 time to fit residues: 18.8321 Evaluate side-chains 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 93 optimal weight: 0.0170 chunk 61 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 339 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.134173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.102307 restraints weight = 25140.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.105313 restraints weight = 14846.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.106962 restraints weight = 10490.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.108921 restraints weight = 8607.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.109550 restraints weight = 7141.513| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9313 Z= 0.123 Angle : 0.605 10.698 12548 Z= 0.311 Chirality : 0.042 0.155 1388 Planarity : 0.004 0.045 1602 Dihedral : 6.615 83.549 1277 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.29 % Allowed : 22.24 % Favored : 73.47 % 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: -0.62 (0.25), residues: 1117 helix: 0.51 (0.21), residues: 579 sheet: -1.69 (0.61), residues: 64 loop : -1.35 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.022 0.001 TYR D 178 PHE 0.022 0.001 PHE B 223 TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9307) covalent geometry : angle 0.60469 (12548) hydrogen bonds : bond 0.03849 ( 469) hydrogen bonds : angle 5.09260 ( 1356) metal coordination : bond 0.00169 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8392 (tptp) cc_final: 0.8035 (mttt) REVERT: A 254 LEU cc_start: 0.7608 (tp) cc_final: 0.7272 (tp) REVERT: A 260 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5957 (ttp80) REVERT: A 507 LYS cc_start: 0.8384 (tppt) cc_final: 0.8088 (tppt) REVERT: A 550 MET cc_start: 0.7684 (mmt) cc_final: 0.7325 (mmt) REVERT: A 668 MET cc_start: 0.6272 (tpp) cc_final: 0.6064 (tpp) REVERT: A 733 LEU cc_start: 0.8223 (mm) cc_final: 0.7884 (tp) REVERT: A 738 PHE cc_start: 0.2217 (m-80) cc_final: -0.0004 (t80) REVERT: C 99 SER cc_start: 0.8961 (m) cc_final: 0.8701 (t) REVERT: C 154 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8647 (mm-30) REVERT: D 89 GLU cc_start: 0.8395 (tt0) cc_final: 0.8072 (mt-10) REVERT: D 90 LEU cc_start: 0.9254 (pp) cc_final: 0.8622 (tp) REVERT: D 92 ASP cc_start: 0.8548 (m-30) cc_final: 0.7539 (t0) REVERT: D 96 ASP cc_start: 0.8240 (m-30) cc_final: 0.7873 (m-30) REVERT: D 174 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8161 (t80) REVERT: D 219 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8583 (mm110) outliers start: 42 outliers final: 22 residues processed: 214 average time/residue: 0.0647 time to fit residues: 20.7853 Evaluate side-chains 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 89 optimal weight: 6.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN D 164 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.133606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.102096 restraints weight = 25132.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.105127 restraints weight = 14806.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.107325 restraints weight = 10416.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.108633 restraints weight = 8158.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109995 restraints weight = 6993.783| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9313 Z= 0.124 Angle : 0.616 9.423 12548 Z= 0.317 Chirality : 0.043 0.182 1388 Planarity : 0.004 0.037 1602 Dihedral : 6.270 81.467 1272 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.98 % Allowed : 23.37 % Favored : 72.65 % 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: -0.58 (0.25), residues: 1117 helix: 0.56 (0.21), residues: 585 sheet: -1.57 (0.62), residues: 64 loop : -1.39 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.016 0.001 TYR D 178 PHE 0.022 0.001 PHE B 223 TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9307) covalent geometry : angle 0.61602 (12548) hydrogen bonds : bond 0.03769 ( 469) hydrogen bonds : angle 5.08098 ( 1356) metal coordination : bond 0.00199 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8358 (tptp) cc_final: 0.8026 (mttt) REVERT: A 243 PHE cc_start: 0.8453 (m-10) cc_final: 0.8206 (m-10) REVERT: A 507 LYS cc_start: 0.8418 (tppt) cc_final: 0.8002 (tppt) REVERT: A 550 MET cc_start: 0.7710 (mmt) cc_final: 0.7401 (mmt) REVERT: A 570 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: A 578 LYS cc_start: 0.8484 (mttm) cc_final: 0.8141 (mtpp) REVERT: A 668 MET cc_start: 0.6331 (tpp) cc_final: 0.6068 (tpp) REVERT: A 733 LEU cc_start: 0.8257 (mm) cc_final: 0.7953 (tp) REVERT: A 738 PHE cc_start: 0.1956 (m-80) cc_final: -0.0119 (t80) REVERT: B 235 LEU cc_start: 0.8699 (mm) cc_final: 0.8473 (mm) REVERT: B 256 MET cc_start: 0.7373 (mmm) cc_final: 0.6322 (mpp) REVERT: C 99 SER cc_start: 0.8951 (m) cc_final: 0.8688 (t) REVERT: C 154 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: D 50 ASN cc_start: 0.7606 (m-40) cc_final: 0.7392 (m-40) REVERT: D 89 GLU cc_start: 0.8428 (tt0) cc_final: 0.8119 (mt-10) REVERT: D 90 LEU cc_start: 0.9257 (pp) cc_final: 0.8638 (tp) REVERT: D 92 ASP cc_start: 0.8560 (m-30) cc_final: 0.7518 (t0) REVERT: D 96 ASP cc_start: 0.8251 (m-30) cc_final: 0.7865 (m-30) REVERT: D 174 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8134 (t80) REVERT: D 219 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8673 (mm110) outliers start: 39 outliers final: 25 residues processed: 209 average time/residue: 0.0635 time to fit residues: 20.2246 Evaluate side-chains 192 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 339 ASN D 219 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.133385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.102111 restraints weight = 24680.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.105338 restraints weight = 14131.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107739 restraints weight = 9744.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109044 restraints weight = 7495.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.109950 restraints weight = 6374.145| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9313 Z= 0.140 Angle : 0.647 12.006 12548 Z= 0.326 Chirality : 0.043 0.175 1388 Planarity : 0.004 0.037 1602 Dihedral : 6.247 74.839 1272 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.78 % Allowed : 24.80 % Favored : 71.43 % 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: -0.46 (0.25), residues: 1117 helix: 0.67 (0.21), residues: 579 sheet: -1.41 (0.58), residues: 71 loop : -1.34 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.014 0.001 TYR D 178 PHE 0.022 0.001 PHE B 223 TRP 0.011 0.001 TRP A 216 HIS 0.007 0.001 HIS D 164 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9307) covalent geometry : angle 0.64749 (12548) hydrogen bonds : bond 0.03833 ( 469) hydrogen bonds : angle 5.09845 ( 1356) metal coordination : bond 0.00325 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8450 (tptp) cc_final: 0.8111 (mttt) REVERT: A 243 PHE cc_start: 0.8431 (m-10) cc_final: 0.8180 (m-10) REVERT: A 260 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5671 (mmm-85) REVERT: A 507 LYS cc_start: 0.8397 (tppt) cc_final: 0.7968 (tppt) REVERT: A 570 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8058 (mtmt) REVERT: A 578 LYS cc_start: 0.8508 (mttm) cc_final: 0.8273 (pttt) REVERT: A 668 MET cc_start: 0.6295 (tpp) cc_final: 0.6031 (tpp) REVERT: A 733 LEU cc_start: 0.8343 (mm) cc_final: 0.8052 (tp) REVERT: B 235 LEU cc_start: 0.8697 (mm) cc_final: 0.8437 (mm) REVERT: B 256 MET cc_start: 0.7384 (mmm) cc_final: 0.6219 (mpp) REVERT: C 99 SER cc_start: 0.8990 (m) cc_final: 0.8714 (t) REVERT: C 154 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (mm-30) REVERT: D 89 GLU cc_start: 0.8461 (tt0) cc_final: 0.8061 (mt-10) REVERT: D 90 LEU cc_start: 0.9269 (pp) cc_final: 0.8659 (tp) REVERT: D 174 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 219 GLN cc_start: 0.8909 (mm110) cc_final: 0.8615 (mm110) outliers start: 37 outliers final: 27 residues processed: 200 average time/residue: 0.0691 time to fit residues: 20.6218 Evaluate side-chains 189 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 1 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.134606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.103141 restraints weight = 25363.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106286 restraints weight = 14622.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.107972 restraints weight = 10186.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109765 restraints weight = 8317.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.110544 restraints weight = 6990.592| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9313 Z= 0.123 Angle : 0.640 10.968 12548 Z= 0.322 Chirality : 0.042 0.159 1388 Planarity : 0.004 0.037 1602 Dihedral : 6.123 68.562 1272 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.88 % Allowed : 25.92 % Favored : 70.20 % 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: -0.33 (0.25), residues: 1117 helix: 0.79 (0.21), residues: 581 sheet: -1.32 (0.59), residues: 71 loop : -1.30 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.014 0.001 TYR D 178 PHE 0.022 0.001 PHE B 223 TRP 0.009 0.001 TRP A 216 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9307) covalent geometry : angle 0.64003 (12548) hydrogen bonds : bond 0.03679 ( 469) hydrogen bonds : angle 5.01802 ( 1356) metal coordination : bond 0.00139 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8388 (tptp) cc_final: 0.8055 (mttt) REVERT: A 243 PHE cc_start: 0.8338 (m-10) cc_final: 0.8118 (m-10) REVERT: A 254 LEU cc_start: 0.7619 (tp) cc_final: 0.7254 (tp) REVERT: A 260 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.6022 (ttp80) REVERT: A 507 LYS cc_start: 0.8448 (tppt) cc_final: 0.7609 (tppt) REVERT: A 570 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: A 578 LYS cc_start: 0.8452 (mttm) cc_final: 0.8219 (pttt) REVERT: A 668 MET cc_start: 0.6336 (tpp) cc_final: 0.6121 (tpp) REVERT: A 733 LEU cc_start: 0.8280 (mm) cc_final: 0.7984 (tp) REVERT: B 235 LEU cc_start: 0.8777 (mm) cc_final: 0.8508 (mm) REVERT: B 256 MET cc_start: 0.7306 (mmm) cc_final: 0.6271 (mpp) REVERT: C 99 SER cc_start: 0.9053 (m) cc_final: 0.8776 (t) REVERT: C 154 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: D 89 GLU cc_start: 0.8371 (tt0) cc_final: 0.8098 (mt-10) REVERT: D 90 LEU cc_start: 0.9264 (pp) cc_final: 0.8692 (tp) REVERT: D 174 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8136 (t80) outliers start: 38 outliers final: 25 residues processed: 204 average time/residue: 0.0732 time to fit residues: 21.9323 Evaluate side-chains 194 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099059 restraints weight = 24949.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102294 restraints weight = 14149.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.104501 restraints weight = 9856.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.105995 restraints weight = 7739.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106827 restraints weight = 6570.669| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9313 Z= 0.159 Angle : 0.692 15.661 12548 Z= 0.348 Chirality : 0.043 0.181 1388 Planarity : 0.004 0.036 1602 Dihedral : 6.127 64.842 1272 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.29 % Allowed : 25.82 % Favored : 69.90 % 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: -0.37 (0.25), residues: 1117 helix: 0.67 (0.21), residues: 587 sheet: -1.14 (0.61), residues: 71 loop : -1.26 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.016 0.002 TYR A 266 PHE 0.022 0.002 PHE B 223 TRP 0.012 0.001 TRP A 216 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9307) covalent geometry : angle 0.69215 (12548) hydrogen bonds : bond 0.03884 ( 469) hydrogen bonds : angle 5.19400 ( 1356) metal coordination : bond 0.00373 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8424 (tptp) cc_final: 0.8092 (mttt) REVERT: A 243 PHE cc_start: 0.8371 (m-10) cc_final: 0.8137 (m-10) REVERT: A 260 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5787 (mmm-85) REVERT: A 507 LYS cc_start: 0.8469 (tppt) cc_final: 0.7628 (tppt) REVERT: A 570 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: A 578 LYS cc_start: 0.8505 (mttm) cc_final: 0.8210 (mtpp) REVERT: A 668 MET cc_start: 0.6382 (tpp) cc_final: 0.6077 (tpp) REVERT: A 733 LEU cc_start: 0.8407 (mm) cc_final: 0.8123 (tp) REVERT: B 223 PHE cc_start: 0.7560 (t80) cc_final: 0.7123 (t80) REVERT: B 235 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8491 (mm) REVERT: B 256 MET cc_start: 0.7239 (mmm) cc_final: 0.6181 (mpp) REVERT: C 99 SER cc_start: 0.9124 (m) cc_final: 0.8836 (t) REVERT: C 154 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8630 (mm-30) REVERT: D 89 GLU cc_start: 0.8482 (tt0) cc_final: 0.8197 (mt-10) REVERT: D 90 LEU cc_start: 0.9269 (pp) cc_final: 0.8702 (tp) REVERT: D 174 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8206 (t80) outliers start: 42 outliers final: 31 residues processed: 199 average time/residue: 0.0713 time to fit residues: 21.0506 Evaluate side-chains 197 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.133467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102555 restraints weight = 24897.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.105684 restraints weight = 14027.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.107953 restraints weight = 9629.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.109114 restraints weight = 7455.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.110512 restraints weight = 6366.876| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9313 Z= 0.152 Angle : 0.686 14.224 12548 Z= 0.346 Chirality : 0.043 0.212 1388 Planarity : 0.004 0.037 1602 Dihedral : 6.161 60.652 1272 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.57 % Allowed : 26.94 % Favored : 69.49 % 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: -0.29 (0.26), residues: 1117 helix: 0.73 (0.21), residues: 584 sheet: -1.14 (0.63), residues: 69 loop : -1.20 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.014 0.002 TYR A 266 PHE 0.023 0.002 PHE B 223 TRP 0.013 0.001 TRP A 216 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9307) covalent geometry : angle 0.68622 (12548) hydrogen bonds : bond 0.03817 ( 469) hydrogen bonds : angle 5.15775 ( 1356) metal coordination : bond 0.00280 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8435 (tptp) cc_final: 0.8121 (mttt) REVERT: A 243 PHE cc_start: 0.8395 (m-10) cc_final: 0.8139 (m-10) REVERT: A 260 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6110 (tpt-90) REVERT: A 507 LYS cc_start: 0.8470 (tppt) cc_final: 0.7698 (tppt) REVERT: A 578 LYS cc_start: 0.8473 (mttm) cc_final: 0.8180 (mtpp) REVERT: A 668 MET cc_start: 0.6482 (tpp) cc_final: 0.6142 (tpp) REVERT: A 733 LEU cc_start: 0.8473 (mm) cc_final: 0.8140 (tp) REVERT: B 223 PHE cc_start: 0.7629 (t80) cc_final: 0.7162 (t80) REVERT: B 235 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8482 (mm) REVERT: B 256 MET cc_start: 0.7247 (mmm) cc_final: 0.6246 (mpp) REVERT: C 99 SER cc_start: 0.9169 (m) cc_final: 0.8851 (t) REVERT: C 154 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8627 (mm-30) REVERT: D 89 GLU cc_start: 0.8592 (tt0) cc_final: 0.8268 (mt-10) REVERT: D 90 LEU cc_start: 0.9268 (pp) cc_final: 0.8714 (tp) REVERT: D 174 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8275 (t80) outliers start: 35 outliers final: 28 residues processed: 195 average time/residue: 0.0686 time to fit residues: 19.5045 Evaluate side-chains 191 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 0.0270 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.130699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097704 restraints weight = 25432.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.100904 restraints weight = 14566.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.103062 restraints weight = 10241.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104528 restraints weight = 8189.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.105313 restraints weight = 7012.800| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9313 Z= 0.173 Angle : 0.709 13.952 12548 Z= 0.359 Chirality : 0.044 0.191 1388 Planarity : 0.004 0.037 1602 Dihedral : 6.180 57.518 1272 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.47 % Allowed : 27.04 % Favored : 69.49 % 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: -0.36 (0.26), residues: 1117 helix: 0.65 (0.21), residues: 593 sheet: -1.02 (0.64), residues: 69 loop : -1.25 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.016 0.002 TYR A 266 PHE 0.021 0.002 PHE B 223 TRP 0.013 0.001 TRP A 216 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9307) covalent geometry : angle 0.70856 (12548) hydrogen bonds : bond 0.03890 ( 469) hydrogen bonds : angle 5.21664 ( 1356) metal coordination : bond 0.00348 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8515 (tptp) cc_final: 0.8180 (mttt) REVERT: A 243 PHE cc_start: 0.8384 (m-10) cc_final: 0.8142 (m-10) REVERT: A 260 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5771 (mmm-85) REVERT: A 507 LYS cc_start: 0.8500 (tppt) cc_final: 0.7758 (tppt) REVERT: A 578 LYS cc_start: 0.8458 (mttm) cc_final: 0.8163 (mtpp) REVERT: A 668 MET cc_start: 0.6447 (tpp) cc_final: 0.6108 (tpp) REVERT: A 693 MET cc_start: 0.7207 (ttp) cc_final: 0.6952 (tmm) REVERT: A 733 LEU cc_start: 0.8520 (mm) cc_final: 0.8221 (tp) REVERT: B 223 PHE cc_start: 0.7686 (t80) cc_final: 0.7148 (t80) REVERT: B 235 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 256 MET cc_start: 0.7182 (mmm) cc_final: 0.6191 (mpp) REVERT: C 154 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: D 89 GLU cc_start: 0.8575 (tt0) cc_final: 0.8299 (mt-10) REVERT: D 90 LEU cc_start: 0.9328 (pp) cc_final: 0.8719 (tp) REVERT: D 174 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8321 (t80) outliers start: 34 outliers final: 29 residues processed: 187 average time/residue: 0.0671 time to fit residues: 18.7564 Evaluate side-chains 188 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.128902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.095771 restraints weight = 25283.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.098748 restraints weight = 14902.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.100830 restraints weight = 10581.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102242 restraints weight = 8492.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.102978 restraints weight = 7328.893| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9313 Z= 0.217 Angle : 0.750 12.849 12548 Z= 0.382 Chirality : 0.046 0.195 1388 Planarity : 0.004 0.038 1602 Dihedral : 6.429 56.205 1272 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.67 % Allowed : 26.53 % Favored : 69.80 % 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: -0.56 (0.25), residues: 1117 helix: 0.49 (0.21), residues: 596 sheet: -1.07 (0.65), residues: 68 loop : -1.39 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 662 TYR 0.021 0.002 TYR A 266 PHE 0.022 0.002 PHE B 223 TRP 0.012 0.002 TRP A 619 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9307) covalent geometry : angle 0.75015 (12548) hydrogen bonds : bond 0.04153 ( 469) hydrogen bonds : angle 5.35346 ( 1356) metal coordination : bond 0.00545 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1550.62 seconds wall clock time: 27 minutes 32.37 seconds (1652.37 seconds total)