Starting phenix.real_space_refine on Thu Jul 2 06:13:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1o_36797/07_2026/8k1o_36797.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 21 5.16 5 C 4572 2.51 5 N 1248 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7163 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3718 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 20, 'TRANS': 489} Chain breaks: 1 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1624 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1597 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 160 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.18, per 1000 atoms: 0.16 Number of scatterers: 7163 At special positions: 0 Unit cell: (72.16, 110.7, 82.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 10 15.00 Mg 2 11.99 O 1310 8.00 N 1248 7.00 C 4572 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: 0.40 Conformation dependent library (CDL) restraints added in 328.4 milliseconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 57.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.564A pdb=" N VAL A 60 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.534A pdb=" N ALA A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.520A pdb=" N ARG A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 127 removed outlier: 3.698A pdb=" N LEU A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.823A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 168 removed outlier: 3.517A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 200 removed outlier: 3.625A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 228 removed outlier: 3.587A pdb=" N VAL A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.520A pdb=" N SER A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.579A pdb=" N VAL A 245 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 273 removed outlier: 3.851A pdb=" N LEU A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 329 removed outlier: 3.523A pdb=" N ASN A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 354 through 389 removed outlier: 3.645A pdb=" N GLN A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.548A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 437 removed outlier: 3.897A pdb=" N SER A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.762A pdb=" N VAL A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 4.301A pdb=" N LEU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.744A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.646A pdb=" N LEU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.535A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.604A pdb=" N ALA B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.602A pdb=" N VAL B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 184 removed outlier: 3.990A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.683A pdb=" N ALA B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.772A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.605A pdb=" N TYR C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.623A pdb=" N LYS C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 184 removed outlier: 3.564A pdb=" N ARG C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 202 removed outlier: 3.655A pdb=" N ALA C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 32 removed outlier: 4.900A pdb=" N LEU B 15 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 29 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG B 13 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 31 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU B 11 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 15 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY B 63 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.789A pdb=" N ALA B 85 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP B 160 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 87 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 157 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER B 191 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 159 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 38 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 205 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 216 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 207 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.568A pdb=" N ILE C 10 " --> pdb=" O VAL C 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 26 removed outlier: 4.701A pdb=" N LEU C 15 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 63 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.482A pdb=" N HIS C 38 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 85 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208 removed outlier: 7.089A pdb=" N VAL C 205 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER C 216 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 207 " --> pdb=" O VAL C 214 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 978 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: 0.73 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1124 1.30 - 1.43: 1767 1.43 - 1.55: 4340 1.55 - 1.68: 21 1.68 - 1.81: 38 Bond restraints: 7290 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" CA ALA A 275 " pdb=" CB ALA A 275 " ideal model delta sigma weight residual 1.530 1.449 0.082 1.48e-02 4.57e+03 3.06e+01 bond pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 9765 3.90 - 7.80: 108 7.80 - 11.70: 19 11.70 - 15.59: 2 15.59 - 19.49: 2 Bond angle restraints: 9896 Sorted by residual: angle pdb=" N ASP A 66 " pdb=" CA ASP A 66 " pdb=" C ASP A 66 " ideal model delta sigma weight residual 110.50 99.12 11.38 1.41e+00 5.03e-01 6.52e+01 angle pdb=" C GLY A 280 " pdb=" N ALA A 281 " pdb=" CA ALA A 281 " ideal model delta sigma weight residual 122.73 109.68 13.05 1.92e+00 2.71e-01 4.62e+01 angle pdb=" PB ANP B 401 " pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 126.95 107.46 19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" N ASN B 172 " pdb=" CA ASN B 172 " pdb=" C ASN B 172 " ideal model delta sigma weight residual 113.88 106.31 7.57 1.23e+00 6.61e-01 3.79e+01 angle pdb=" N PRO A 65 " pdb=" CA PRO A 65 " pdb=" C PRO A 65 " ideal model delta sigma weight residual 112.47 124.70 -12.23 2.06e+00 2.36e-01 3.52e+01 ... (remaining 9891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 4209 32.23 - 64.46: 157 64.46 - 96.69: 28 96.69 - 128.92: 2 128.92 - 161.15: 1 Dihedral angle restraints: 4397 sinusoidal: 1791 harmonic: 2606 Sorted by residual: dihedral pdb=" CA CYS B 202 " pdb=" C CYS B 202 " pdb=" N GLU B 203 " pdb=" CA GLU B 203 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" O1A ANP C 401 " pdb=" O3A ANP C 401 " pdb=" PA ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sinusoidal sigma weight residual 83.11 -78.04 161.15 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA GLY A 240 " pdb=" C GLY A 240 " pdb=" N TRP A 241 " pdb=" CA TRP A 241 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 4394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1093 0.096 - 0.192: 64 0.192 - 0.288: 8 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA ASN C 44 " pdb=" N ASN C 44 " pdb=" C ASN C 44 " pdb=" CB ASN C 44 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA ASP A 66 " pdb=" N ASP A 66 " pdb=" C ASP A 66 " pdb=" CB ASP A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1164 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 136 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C TYR B 136 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR B 136 " 0.016 2.00e-02 2.50e+03 pdb=" N SER B 137 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 64 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C TYR A 64 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 64 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 34 " -0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLU B 34 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU B 34 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY B 35 " -0.012 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 34 2.54 - 3.13: 5189 3.13 - 3.72: 10285 3.72 - 4.31: 14996 4.31 - 4.90: 26269 Nonbonded interactions: 56773 Sorted by model distance: nonbonded pdb=" OG SER C 49 " pdb="MG MG C 402 " model vdw 1.945 2.170 nonbonded pdb=" O3G ANP C 401 " pdb="MG MG C 402 " model vdw 2.034 2.170 nonbonded pdb=" OG SER B 49 " pdb="MG MG B 402 " model vdw 2.039 2.170 nonbonded pdb=" O3G ANP B 401 " pdb="MG MG B 402 " model vdw 2.078 2.170 nonbonded pdb=" O2B ANP C 401 " pdb=" O3G ANP C 401 " model vdw 2.137 3.040 ... (remaining 56768 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 'B' and resid 8 through 402) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.130 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.007 0.146 7290 Z= 0.392 Angle : 1.018 19.492 9896 Z= 0.546 Chirality : 0.052 0.480 1167 Planarity : 0.005 0.040 1225 Dihedral : 17.209 161.154 2739 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.42 % Allowed : 0.14 % Favored : 99.44 % 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: -1.93 (0.27), residues: 929 helix: -0.47 (0.23), residues: 528 sheet: -1.51 (0.70), residues: 58 loop : -2.46 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 382 TYR 0.008 0.001 TYR C 86 PHE 0.022 0.001 PHE C 40 TRP 0.022 0.001 TRP A 44 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.39 ( 7290) covalent geometry : angle 1.01800 / 0.55 ( 9896) hydrogen bonds : bond 0.17522 / 12.19 ( 331) hydrogen bonds : angle 6.47972 / 4.66 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.257 Fit side-chains REVERT: A 39 VAL cc_start: 0.8528 (m) cc_final: 0.8227 (p) REVERT: A 105 MET cc_start: 0.8016 (tpp) cc_final: 0.7703 (tpt) REVERT: A 128 SER cc_start: 0.8006 (m) cc_final: 0.7659 (p) REVERT: A 159 THR cc_start: 0.8254 (t) cc_final: 0.7771 (m) REVERT: A 272 ARG cc_start: 0.6630 (mmp-170) cc_final: 0.6199 (mpt180) REVERT: A 393 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7554 (pt0) REVERT: B 23 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6740 (mtp85) REVERT: B 124 ARG cc_start: 0.8213 (ptp-110) cc_final: 0.7967 (ptm160) REVERT: B 171 GLU cc_start: 0.7685 (pp20) cc_final: 0.7107 (tm-30) REVERT: C 67 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7183 (mmp80) REVERT: C 176 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7112 (mt0) REVERT: C 182 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6988 (ttm170) outliers start: 3 outliers final: 2 residues processed: 151 average time/residue: 0.5551 time to fit residues: 87.5643 Evaluate side-chains 99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.096223 restraints weight = 8582.934| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.44 r_work: 0.2897 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.144 Angle : 0.615 8.631 9896 Z= 0.305 Chirality : 0.043 0.151 1167 Planarity : 0.005 0.041 1225 Dihedral : 14.770 136.513 1258 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.69 % Allowed : 11.14 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.08 (0.28), residues: 929 helix: 0.26 (0.23), residues: 539 sheet: -1.10 (0.65), residues: 70 loop : -2.28 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 23 TYR 0.008 0.001 TYR A 56 PHE 0.013 0.001 PHE C 40 TRP 0.020 0.001 TRP A 44 HIS 0.008 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 7290) covalent geometry : angle 0.61526 / 0.31 ( 9896) hydrogen bonds : bond 0.04715 / 3.21 ( 331) hydrogen bonds : angle 3.80687 / 2.76 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.203 Fit side-chains REVERT: A 105 MET cc_start: 0.8442 (tpp) cc_final: 0.8076 (tpt) REVERT: A 120 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8308 (ttt-90) REVERT: A 128 SER cc_start: 0.7926 (m) cc_final: 0.7653 (p) REVERT: A 272 ARG cc_start: 0.7212 (mmp-170) cc_final: 0.6954 (tmt-80) REVERT: A 314 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 23 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7139 (mtp85) REVERT: B 26 ASP cc_start: 0.8185 (m-30) cc_final: 0.7859 (t0) REVERT: C 67 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7617 (mmp80) REVERT: C 176 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7339 (mt0) REVERT: C 182 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7276 (ttm170) REVERT: C 199 GLU cc_start: 0.8088 (pt0) cc_final: 0.7771 (pp20) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.5038 time to fit residues: 54.9125 Evaluate side-chains 99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.096126 restraints weight = 8523.707| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.45 r_work: 0.2888 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.132 Angle : 0.576 8.457 9896 Z= 0.285 Chirality : 0.042 0.140 1167 Planarity : 0.004 0.040 1225 Dihedral : 12.650 122.206 1257 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.12 % Allowed : 13.82 % Favored : 84.06 % 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: -0.69 (0.28), residues: 929 helix: 0.62 (0.24), residues: 538 sheet: -0.82 (0.67), residues: 70 loop : -2.23 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 67 TYR 0.012 0.001 TYR A 432 PHE 0.010 0.001 PHE C 40 TRP 0.020 0.001 TRP A 44 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 7290) covalent geometry : angle 0.57637 / 0.28 ( 9896) hydrogen bonds : bond 0.04302 / 2.92 ( 331) hydrogen bonds : angle 3.53535 / 2.57 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.182 Fit side-chains REVERT: A 93 ASP cc_start: 0.8870 (p0) cc_final: 0.8620 (p0) REVERT: A 105 MET cc_start: 0.8484 (tpp) cc_final: 0.8103 (tpt) REVERT: A 120 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8290 (ttt-90) REVERT: A 128 SER cc_start: 0.7838 (m) cc_final: 0.7602 (p) REVERT: A 314 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8344 (tp) REVERT: B 23 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7215 (mtp85) REVERT: B 26 ASP cc_start: 0.8237 (m-30) cc_final: 0.7997 (t0) REVERT: B 171 GLU cc_start: 0.8176 (pt0) cc_final: 0.7590 (tp30) REVERT: B 172 ASN cc_start: 0.8334 (t0) cc_final: 0.8045 (t0) REVERT: C 26 ASP cc_start: 0.8228 (t70) cc_final: 0.8007 (t70) REVERT: C 67 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7684 (mmp80) REVERT: C 176 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7367 (mt0) REVERT: C 182 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: C 199 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: C 212 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8618 (ptpt) outliers start: 15 outliers final: 5 residues processed: 103 average time/residue: 0.5585 time to fit residues: 60.1182 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 31 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.095874 restraints weight = 8578.984| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.46 r_work: 0.2876 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.134 Angle : 0.564 8.721 9896 Z= 0.280 Chirality : 0.042 0.142 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.907 117.754 1256 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.83 % Allowed : 15.66 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.28), residues: 929 helix: 0.76 (0.24), residues: 534 sheet: -0.65 (0.69), residues: 67 loop : -2.10 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.008 0.001 TYR A 56 PHE 0.010 0.001 PHE C 19 TRP 0.019 0.001 TRP A 44 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 7290) covalent geometry : angle 0.56362 / 0.28 ( 9896) hydrogen bonds : bond 0.04255 / 2.89 ( 331) hydrogen bonds : angle 3.45553 / 2.52 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.172 Fit side-chains REVERT: A 93 ASP cc_start: 0.8856 (p0) cc_final: 0.8562 (p0) REVERT: A 105 MET cc_start: 0.8524 (tpp) cc_final: 0.8145 (tpt) REVERT: A 120 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8280 (ttt-90) REVERT: A 314 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8348 (tp) REVERT: B 23 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7194 (mtp85) REVERT: B 26 ASP cc_start: 0.8183 (m-30) cc_final: 0.7945 (t0) REVERT: B 171 GLU cc_start: 0.8141 (pt0) cc_final: 0.7635 (tp30) REVERT: B 172 ASN cc_start: 0.8236 (t0) cc_final: 0.8005 (t0) REVERT: C 26 ASP cc_start: 0.8254 (t70) cc_final: 0.7970 (t0) REVERT: C 67 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7695 (mmp80) REVERT: C 176 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7323 (mt0) REVERT: C 199 GLU cc_start: 0.8180 (pt0) cc_final: 0.7898 (pp20) REVERT: C 212 LYS cc_start: 0.8905 (ptpp) cc_final: 0.8639 (ptpt) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.5403 time to fit residues: 53.0822 Evaluate side-chains 89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101582 restraints weight = 8405.812| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.58 r_work: 0.2923 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.130 Angle : 0.545 8.676 9896 Z= 0.273 Chirality : 0.041 0.131 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.570 117.512 1256 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % 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: -0.35 (0.28), residues: 929 helix: 0.87 (0.24), residues: 534 sheet: -0.85 (0.74), residues: 62 loop : -1.92 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.007 0.001 TYR A 56 PHE 0.010 0.001 PHE C 19 TRP 0.026 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7290) covalent geometry : angle 0.54547 / 0.27 ( 9896) hydrogen bonds : bond 0.04139 / 2.81 ( 331) hydrogen bonds : angle 3.40794 / 2.49 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.161 Fit side-chains REVERT: A 93 ASP cc_start: 0.8902 (p0) cc_final: 0.8639 (p0) REVERT: A 105 MET cc_start: 0.8554 (tpp) cc_final: 0.8210 (tpt) REVERT: A 120 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8278 (ttt-90) REVERT: A 314 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 23 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7186 (mtp85) REVERT: B 171 GLU cc_start: 0.8117 (pt0) cc_final: 0.7749 (tp30) REVERT: B 172 ASN cc_start: 0.8249 (t0) cc_final: 0.8036 (t0) REVERT: C 26 ASP cc_start: 0.8258 (t70) cc_final: 0.7947 (t0) REVERT: C 67 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7666 (mmp80) REVERT: C 176 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7420 (mt0) REVERT: C 199 GLU cc_start: 0.8164 (pt0) cc_final: 0.7904 (pp20) REVERT: C 212 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8615 (ptpt) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.5822 time to fit residues: 55.2792 Evaluate side-chains 90 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 chunk 28 optimal weight: 0.6980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104396 restraints weight = 8318.797| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.59 r_work: 0.2952 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7290 Z= 0.096 Angle : 0.486 7.794 9896 Z= 0.248 Chirality : 0.039 0.126 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.051 113.190 1256 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.69 % Allowed : 17.49 % Favored : 80.82 % 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: -0.05 (0.28), residues: 929 helix: 1.14 (0.24), residues: 534 sheet: -0.78 (0.74), residues: 62 loop : -1.86 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 67 TYR 0.013 0.001 TYR A 432 PHE 0.007 0.001 PHE A 360 TRP 0.026 0.001 TRP A 44 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7290) covalent geometry : angle 0.48594 / 0.25 ( 9896) hydrogen bonds : bond 0.03288 / 2.23 ( 331) hydrogen bonds : angle 3.26899 / 2.39 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.188 Fit side-chains REVERT: A 93 ASP cc_start: 0.8857 (p0) cc_final: 0.8598 (p0) REVERT: A 105 MET cc_start: 0.8548 (tpp) cc_final: 0.8157 (tpt) REVERT: A 120 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8241 (ttt-90) REVERT: A 314 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 370 MET cc_start: 0.8197 (mtt) cc_final: 0.7934 (mtt) REVERT: A 500 MET cc_start: 0.7715 (tpt) cc_final: 0.7044 (ptt) REVERT: B 23 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7109 (mtp85) REVERT: B 26 ASP cc_start: 0.8152 (t0) cc_final: 0.7926 (t0) REVERT: B 171 GLU cc_start: 0.7977 (pt0) cc_final: 0.7618 (tp30) REVERT: B 172 ASN cc_start: 0.8132 (t0) cc_final: 0.7896 (t0) REVERT: C 26 ASP cc_start: 0.8212 (t70) cc_final: 0.7854 (t0) REVERT: C 67 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7568 (mmp80) REVERT: C 176 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7327 (mt0) REVERT: C 199 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7778 (pp20) outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 0.5472 time to fit residues: 52.5423 Evaluate side-chains 89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN C 18 HIS C 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101835 restraints weight = 8328.121| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.57 r_work: 0.2913 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.127 Angle : 0.535 7.014 9896 Z= 0.270 Chirality : 0.041 0.127 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.293 115.427 1256 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.40 % Allowed : 17.35 % Favored : 80.25 % 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: -0.04 (0.28), residues: 929 helix: 1.13 (0.24), residues: 528 sheet: -0.74 (0.74), residues: 62 loop : -1.77 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.007 0.001 TYR A 56 PHE 0.009 0.001 PHE C 19 TRP 0.027 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7290) covalent geometry : angle 0.53481 / 0.27 ( 9896) hydrogen bonds : bond 0.04047 / 2.76 ( 331) hydrogen bonds : angle 3.32317 / 2.43 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8870 (p0) cc_final: 0.8630 (p0) REVERT: A 105 MET cc_start: 0.8535 (tpp) cc_final: 0.8130 (tpt) REVERT: A 120 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8239 (ttt-90) REVERT: A 314 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 500 MET cc_start: 0.7690 (tpt) cc_final: 0.7021 (ptt) REVERT: B 23 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7219 (mtp85) REVERT: B 26 ASP cc_start: 0.8244 (t0) cc_final: 0.8023 (t0) REVERT: B 171 GLU cc_start: 0.8006 (pt0) cc_final: 0.7719 (tp30) REVERT: C 26 ASP cc_start: 0.8253 (t70) cc_final: 0.7898 (t0) REVERT: C 67 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7669 (mmp80) REVERT: C 176 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7437 (mt0) REVERT: C 199 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7859 (pp20) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.5793 time to fit residues: 55.4860 Evaluate side-chains 87 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN C 18 HIS C 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101419 restraints weight = 8388.604| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.59 r_work: 0.2908 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.136 Angle : 0.549 7.050 9896 Z= 0.278 Chirality : 0.041 0.129 1167 Planarity : 0.004 0.042 1225 Dihedral : 11.418 115.523 1256 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.12 % Allowed : 17.91 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 929 helix: 1.13 (0.23), residues: 528 sheet: -0.72 (0.74), residues: 62 loop : -1.73 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.014 0.001 TYR A 432 PHE 0.010 0.001 PHE C 19 TRP 0.030 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7290) covalent geometry : angle 0.54877 / 0.28 ( 9896) hydrogen bonds : bond 0.04167 / 2.84 ( 331) hydrogen bonds : angle 3.36483 / 2.46 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8511 (t) cc_final: 0.8226 (m) REVERT: A 93 ASP cc_start: 0.8881 (p0) cc_final: 0.8664 (p0) REVERT: A 105 MET cc_start: 0.8523 (tpp) cc_final: 0.8114 (tpt) REVERT: A 120 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8279 (ttt-90) REVERT: A 314 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8380 (tp) REVERT: A 370 MET cc_start: 0.8383 (mtt) cc_final: 0.8118 (mtt) REVERT: A 500 MET cc_start: 0.7738 (tpt) cc_final: 0.7053 (ptt) REVERT: B 23 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7167 (mtp85) REVERT: B 26 ASP cc_start: 0.8246 (t0) cc_final: 0.7898 (t0) REVERT: B 172 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: C 26 ASP cc_start: 0.8272 (t70) cc_final: 0.7938 (t0) REVERT: C 67 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7671 (mmp80) REVERT: C 176 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7434 (mt0) REVERT: C 199 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7992 (pp20) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.6117 time to fit residues: 57.4791 Evaluate side-chains 96 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN C 18 HIS C 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104301 restraints weight = 8323.025| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.57 r_work: 0.2946 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7290 Z= 0.103 Angle : 0.499 6.154 9896 Z= 0.258 Chirality : 0.039 0.125 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.036 112.898 1256 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.12 % Allowed : 18.05 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 929 helix: 1.31 (0.23), residues: 535 sheet: -0.64 (0.74), residues: 62 loop : -1.67 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.016 0.001 TYR A 432 PHE 0.007 0.001 PHE C 19 TRP 0.031 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 7290) covalent geometry : angle 0.49917 / 0.26 ( 9896) hydrogen bonds : bond 0.03318 / 2.26 ( 331) hydrogen bonds : angle 3.22634 / 2.36 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8863 (p0) cc_final: 0.8652 (p0) REVERT: A 105 MET cc_start: 0.8504 (tpp) cc_final: 0.8043 (tpt) REVERT: A 120 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8197 (ttt-90) REVERT: A 314 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8217 (tp) REVERT: A 370 MET cc_start: 0.8167 (mtt) cc_final: 0.7899 (mtt) REVERT: A 473 ARG cc_start: 0.8211 (ttp80) cc_final: 0.6061 (pmt170) REVERT: A 500 MET cc_start: 0.7669 (tpt) cc_final: 0.6953 (ptt) REVERT: B 23 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7031 (mtp85) REVERT: B 26 ASP cc_start: 0.8150 (t0) cc_final: 0.7776 (t0) REVERT: B 82 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (mtt180) REVERT: B 172 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7689 (m-40) REVERT: C 23 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6924 (ttp80) REVERT: C 26 ASP cc_start: 0.8151 (t70) cc_final: 0.7913 (t0) REVERT: C 67 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7560 (mmp80) REVERT: C 176 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7264 (mt0) REVERT: C 199 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7951 (pp20) outliers start: 15 outliers final: 6 residues processed: 90 average time/residue: 0.5953 time to fit residues: 55.8070 Evaluate side-chains 88 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.0020 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 HIS C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102190 restraints weight = 8292.420| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.59 r_work: 0.2916 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7290 Z= 0.128 Angle : 0.540 6.456 9896 Z= 0.276 Chirality : 0.041 0.130 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.226 114.839 1256 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.83 % Allowed : 18.19 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.28), residues: 929 helix: 1.30 (0.23), residues: 529 sheet: -0.65 (0.74), residues: 62 loop : -1.62 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.006 0.001 TYR A 56 PHE 0.009 0.001 PHE C 19 TRP 0.030 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7290) covalent geometry : angle 0.54025 / 0.28 ( 9896) hydrogen bonds : bond 0.03922 / 2.67 ( 331) hydrogen bonds : angle 3.30659 / 2.42 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8863 (p0) cc_final: 0.8649 (p0) REVERT: A 105 MET cc_start: 0.8529 (tpp) cc_final: 0.8110 (tpt) REVERT: A 120 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8256 (ttt-90) REVERT: A 314 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 370 MET cc_start: 0.8309 (mtt) cc_final: 0.8058 (mtt) REVERT: A 473 ARG cc_start: 0.8282 (ttp80) cc_final: 0.6149 (pmt170) REVERT: A 500 MET cc_start: 0.7699 (tpt) cc_final: 0.7037 (ptt) REVERT: B 23 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7146 (mtp85) REVERT: B 26 ASP cc_start: 0.8224 (t0) cc_final: 0.7883 (t0) REVERT: B 82 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: B 172 ASN cc_start: 0.8236 (t0) cc_final: 0.7693 (m-40) REVERT: C 23 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7180 (tmm-80) REVERT: C 67 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7744 (mmp80) REVERT: C 176 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7362 (mt0) REVERT: C 199 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7944 (pp20) outliers start: 13 outliers final: 5 residues processed: 84 average time/residue: 0.6368 time to fit residues: 55.8287 Evaluate side-chains 89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 23 ARG Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 HIS C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102089 restraints weight = 8340.348| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.59 r_work: 0.2917 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7290 Z= 0.127 Angle : 0.538 6.415 9896 Z= 0.275 Chirality : 0.041 0.127 1167 Planarity : 0.004 0.041 1225 Dihedral : 11.263 114.681 1256 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.97 % Allowed : 18.05 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.28), residues: 929 helix: 1.38 (0.23), residues: 522 sheet: -0.65 (0.74), residues: 62 loop : -1.65 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 67 TYR 0.018 0.001 TYR A 432 PHE 0.008 0.001 PHE A 365 TRP 0.033 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7290) covalent geometry : angle 0.53804 / 0.27 ( 9896) hydrogen bonds : bond 0.03917 / 2.67 ( 331) hydrogen bonds : angle 3.31475 / 2.42 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.77 seconds wall clock time: 33 minutes 22.48 seconds (2002.48 seconds total)