Starting phenix.real_space_refine on Mon Apr 28 07:18:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_36797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_36797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_36797.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_36797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1o_36797/04_2025/8k1o_36797.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.55, per 1000 atoms: 0.77 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: 2.05 Conformation dependent library (CDL) restraints added in 850.6 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: 0.66 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: 1.94 Time building geometry restraints manager: 2.39 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: 9772 3.90 - 7.80: 102 7.80 - 11.70: 18 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: 4160 32.23 - 64.46: 175 64.46 - 96.69: 26 96.69 - 128.92: 2 128.92 - 161.15: 2 Dihedral angle restraints: 4365 sinusoidal: 1759 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 4362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1091 0.096 - 0.192: 66 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 219 or resid 401 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: 4.210 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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= 0.374 Angle : 0.998 19.492 9896 Z= 0.551 Chirality : 0.052 0.480 1167 Planarity : 0.005 0.040 1225 Dihedral : 17.978 161.154 2707 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.001 TRP A 44 HIS 0.007 0.001 HIS C 193 PHE 0.022 0.001 PHE C 40 TYR 0.008 0.001 TYR C 86 ARG 0.006 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.17522 ( 331) hydrogen bonds : angle 6.47972 ( 978) covalent geometry : bond 0.00689 ( 7290) covalent geometry : angle 0.99835 ( 9896) *********************** 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 : 0.780 Fit side-chains REVERT: A 39 VAL cc_start: 0.8529 (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: 0.7686 (pp20) cc_final: 0.7107 (tm-30) REVERT: C 67 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7182 (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: 1.5499 time to fit residues: 244.0634 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 : 0.838 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3172 r_free = 0.3172 target = 0.111265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.096038 restraints weight = 8413.412| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.43 r_work: 0.2923 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7290 Z= 0.154 Angle : 0.636 9.346 9896 Z= 0.314 Chirality : 0.043 0.153 1167 Planarity : 0.005 0.042 1225 Dihedral : 15.845 134.935 1226 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.12 % Allowed : 11.00 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 929 helix: 0.23 (0.23), residues: 542 sheet: -1.07 (0.65), residues: 70 loop : -2.31 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 44 HIS 0.009 0.001 HIS C 193 PHE 0.014 0.002 PHE C 40 TYR 0.010 0.002 TYR A 56 ARG 0.003 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 331) hydrogen bonds : angle 3.76607 ( 978) covalent geometry : bond 0.00373 ( 7290) covalent geometry : angle 0.63609 ( 9896) *********************** 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 112 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.893 Fit side-chains REVERT: A 93 ASP cc_start: 0.8869 (p0) cc_final: 0.8664 (p0) REVERT: A 105 MET cc_start: 0.8482 (tpp) cc_final: 0.8116 (tpt) REVERT: A 120 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8445 (ttm-80) REVERT: A 128 SER cc_start: 0.7931 (m) cc_final: 0.7678 (p) REVERT: A 133 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 272 ARG cc_start: 0.7239 (mmp-170) cc_final: 0.7025 (tmt-80) REVERT: A 314 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 23 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7201 (mtp85) REVERT: B 26 ASP cc_start: 0.8186 (m-30) cc_final: 0.7855 (t0) REVERT: C 67 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7656 (mmp80) REVERT: C 176 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7384 (mt0) REVERT: C 182 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7315 (ttm170) REVERT: C 199 GLU cc_start: 0.8147 (pt0) cc_final: 0.7772 (pp20) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 1.8068 time to fit residues: 202.6878 Evaluate side-chains 99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 133 LEU 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 164 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 4 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099233 restraints weight = 8449.221| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.44 r_work: 0.2957 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2027 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= 0.098 Angle : 0.519 7.638 9896 Z= 0.261 Chirality : 0.040 0.132 1167 Planarity : 0.004 0.040 1225 Dihedral : 13.882 122.331 1225 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.27 % Allowed : 14.25 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 929 helix: 0.63 (0.24), residues: 545 sheet: -0.82 (0.67), residues: 70 loop : -2.14 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.007 0.001 PHE C 19 TYR 0.013 0.001 TYR A 432 ARG 0.006 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 331) hydrogen bonds : angle 3.48068 ( 978) covalent geometry : bond 0.00219 ( 7290) covalent geometry : angle 0.51916 ( 9896) *********************** 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 104 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.742 Fit side-chains REVERT: A 93 ASP cc_start: 0.8882 (p0) cc_final: 0.8633 (p0) REVERT: A 105 MET cc_start: 0.8525 (tpp) cc_final: 0.8158 (tpt) REVERT: A 120 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8330 (ttt-90) REVERT: A 128 SER cc_start: 0.7862 (m) cc_final: 0.7619 (p) REVERT: A 314 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (tp) REVERT: B 23 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7171 (mtp85) REVERT: B 26 ASP cc_start: 0.8132 (m-30) cc_final: 0.7677 (t0) REVERT: B 171 GLU cc_start: 0.8138 (pt0) cc_final: 0.7501 (tp30) REVERT: B 172 ASN cc_start: 0.8315 (t0) cc_final: 0.8054 (t0) REVERT: C 67 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7690 (mmp80) REVERT: C 176 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7402 (mt0) REVERT: C 182 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.7293 (ttp-110) REVERT: C 199 GLU cc_start: 0.8158 (pt0) cc_final: 0.7889 (pp20) outliers start: 9 outliers final: 2 residues processed: 103 average time/residue: 1.5376 time to fit residues: 165.7620 Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095012 restraints weight = 8518.617| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.44 r_work: 0.2892 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7290 Z= 0.158 Angle : 0.593 9.036 9896 Z= 0.294 Chirality : 0.043 0.150 1167 Planarity : 0.004 0.040 1225 Dihedral : 13.458 120.902 1224 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.83 % Allowed : 14.53 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 929 helix: 0.72 (0.24), residues: 535 sheet: -0.72 (0.68), residues: 70 loop : -2.09 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 44 HIS 0.008 0.001 HIS C 193 PHE 0.012 0.001 PHE C 19 TYR 0.009 0.001 TYR A 56 ARG 0.005 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 331) hydrogen bonds : angle 3.50876 ( 978) covalent geometry : bond 0.00389 ( 7290) covalent geometry : angle 0.59280 ( 9896) *********************** 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 96 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.760 Fit side-chains REVERT: A 93 ASP cc_start: 0.8846 (p0) cc_final: 0.8574 (p0) REVERT: A 105 MET cc_start: 0.8485 (tpp) cc_final: 0.8096 (tpt) REVERT: A 120 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8388 (ttm-80) REVERT: A 128 SER cc_start: 0.7811 (m) cc_final: 0.7598 (p) REVERT: A 314 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 23 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7181 (mtp85) REVERT: B 26 ASP cc_start: 0.8132 (m-30) cc_final: 0.7882 (t0) REVERT: B 172 ASN cc_start: 0.8262 (t0) cc_final: 0.8039 (t0) REVERT: C 67 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7664 (mmp80) REVERT: C 176 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7293 (mt0) REVERT: C 182 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7202 (ttm170) REVERT: C 199 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7950 (pp20) outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 1.5362 time to fit residues: 147.8390 Evaluate side-chains 83 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 60 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102062 restraints weight = 8288.869| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.59 r_work: 0.2919 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7290 Z= 0.119 Angle : 0.520 6.430 9896 Z= 0.264 Chirality : 0.041 0.132 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.824 116.739 1224 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.55 % Allowed : 15.66 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 929 helix: 0.88 (0.23), residues: 535 sheet: -0.83 (0.74), residues: 62 loop : -1.88 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.010 0.001 PHE C 19 TYR 0.006 0.001 TYR A 56 ARG 0.006 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 331) hydrogen bonds : angle 3.38381 ( 978) covalent geometry : bond 0.00286 ( 7290) covalent geometry : angle 0.51959 ( 9896) *********************** 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 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.775 Fit side-chains REVERT: A 93 ASP cc_start: 0.8895 (p0) cc_final: 0.8636 (p0) REVERT: A 105 MET cc_start: 0.8578 (tpp) cc_final: 0.8193 (tpt) REVERT: A 120 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8276 (ttt-90) REVERT: A 314 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8356 (tp) REVERT: B 23 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7155 (mtp85) REVERT: B 171 GLU cc_start: 0.8140 (pt0) cc_final: 0.7706 (tp30) REVERT: B 172 ASN cc_start: 0.8262 (t0) cc_final: 0.8036 (t0) REVERT: C 67 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7659 (mmp80) REVERT: C 176 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7420 (mt0) REVERT: C 199 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: C 212 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8553 (ptpt) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 1.6421 time to fit residues: 156.2865 Evaluate side-chains 88 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 B residue 65 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 199 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102506 restraints weight = 8282.173| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.59 r_work: 0.2926 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7290 Z= 0.115 Angle : 0.509 6.179 9896 Z= 0.259 Chirality : 0.040 0.127 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.489 114.542 1224 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 16.36 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 929 helix: 1.08 (0.23), residues: 528 sheet: -0.81 (0.74), residues: 62 loop : -1.84 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.010 0.001 PHE C 19 TYR 0.013 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 331) hydrogen bonds : angle 3.30945 ( 978) covalent geometry : bond 0.00275 ( 7290) covalent geometry : angle 0.50890 ( 9896) *********************** 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 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8282 (mm110) cc_final: 0.8057 (mm-40) REVERT: A 93 ASP cc_start: 0.8901 (p0) cc_final: 0.8648 (p0) REVERT: A 105 MET cc_start: 0.8546 (tpp) cc_final: 0.8186 (tpt) REVERT: A 120 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8251 (ttt-90) REVERT: A 314 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 370 MET cc_start: 0.8294 (mtt) cc_final: 0.8063 (mtt) REVERT: B 23 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7198 (mtp85) REVERT: B 26 ASP cc_start: 0.8200 (t0) cc_final: 0.7973 (t0) REVERT: B 171 GLU cc_start: 0.8036 (pt0) cc_final: 0.7679 (tp30) REVERT: B 172 ASN cc_start: 0.8258 (t0) cc_final: 0.8046 (t0) REVERT: C 67 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7645 (mmp80) REVERT: C 176 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7424 (mt0) REVERT: C 199 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7823 (pp20) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 1.7003 time to fit residues: 161.4212 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 : 0.937 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 216 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 80 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3219 r_free = 0.3219 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098142 restraints weight = 8430.599| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.57 r_work: 0.2913 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2525 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 : 0.538 7.022 9896 Z= 0.273 Chirality : 0.041 0.130 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.491 115.584 1224 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.54 % Allowed : 16.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 929 helix: 1.13 (0.23), residues: 526 sheet: -0.79 (0.74), residues: 62 loop : -1.80 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.010 0.001 PHE C 19 TYR 0.007 0.001 TYR A 56 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 331) hydrogen bonds : angle 3.33974 ( 978) covalent geometry : bond 0.00316 ( 7290) covalent geometry : angle 0.53838 ( 9896) *********************** 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 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8245 (mm110) cc_final: 0.8006 (mm-40) REVERT: A 93 ASP cc_start: 0.8862 (p0) cc_final: 0.8606 (p0) REVERT: A 105 MET cc_start: 0.8473 (tpp) cc_final: 0.8043 (tpt) REVERT: A 120 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8135 (ttt-90) REVERT: A 314 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 500 MET cc_start: 0.7744 (tpt) cc_final: 0.7004 (ptt) REVERT: B 23 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7108 (mtp85) REVERT: B 26 ASP cc_start: 0.8144 (t0) cc_final: 0.7919 (t0) REVERT: B 171 GLU cc_start: 0.7981 (pt0) cc_final: 0.7640 (tp30) REVERT: B 172 ASN cc_start: 0.8126 (t0) cc_final: 0.7914 (t0) REVERT: C 67 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7537 (mmp80) REVERT: C 176 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7276 (mt0) REVERT: C 199 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7881 (pp20) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 1.7657 time to fit residues: 163.4169 Evaluate side-chains 88 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3215 r_free = 0.3215 target = 0.113524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097600 restraints weight = 8449.919| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.62 r_work: 0.2899 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2580 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 : 0.544 7.051 9896 Z= 0.276 Chirality : 0.041 0.129 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.501 115.805 1224 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.54 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 929 helix: 1.13 (0.23), residues: 527 sheet: -0.77 (0.74), residues: 62 loop : -1.76 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 44 HIS 0.006 0.001 HIS C 193 PHE 0.010 0.001 PHE C 19 TYR 0.015 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 331) hydrogen bonds : angle 3.35386 ( 978) covalent geometry : bond 0.00331 ( 7290) covalent geometry : angle 0.54434 ( 9896) *********************** 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 100 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8378 (mm110) cc_final: 0.8141 (mm-40) REVERT: A 93 ASP cc_start: 0.8880 (p0) cc_final: 0.8638 (p0) REVERT: A 105 MET cc_start: 0.8556 (tpp) cc_final: 0.8149 (tpt) REVERT: A 120 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8270 (ttt-90) REVERT: A 314 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8395 (tp) REVERT: A 370 MET cc_start: 0.8364 (mtt) cc_final: 0.8090 (mtt) REVERT: A 434 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7155 (mtt) REVERT: A 500 MET cc_start: 0.7788 (tpt) cc_final: 0.7106 (ptt) REVERT: B 23 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7172 (mtp85) REVERT: B 26 ASP cc_start: 0.8202 (t0) cc_final: 0.7894 (t0) REVERT: B 82 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7728 (mtt180) REVERT: B 171 GLU cc_start: 0.8022 (pt0) cc_final: 0.7754 (tp30) REVERT: C 67 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7756 (mmp80) REVERT: C 176 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7380 (mt0) REVERT: C 199 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7992 (pp20) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 1.6870 time to fit residues: 163.3474 Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 434 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 164 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3200 r_free = 0.3200 target = 0.112587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096601 restraints weight = 8525.637| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.63 r_work: 0.2943 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7290 Z= 0.138 Angle : 0.552 7.030 9896 Z= 0.281 Chirality : 0.041 0.130 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.496 115.871 1224 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.40 % Allowed : 16.64 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 929 helix: 1.16 (0.23), residues: 527 sheet: -0.75 (0.74), residues: 62 loop : -1.75 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.010 0.001 PHE C 19 TYR 0.007 0.001 TYR A 56 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 331) hydrogen bonds : angle 3.36927 ( 978) covalent geometry : bond 0.00336 ( 7290) covalent geometry : angle 0.55197 ( 9896) *********************** 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 101 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8505 (t) cc_final: 0.8223 (m) REVERT: A 83 GLN cc_start: 0.8379 (mm110) cc_final: 0.8135 (mm-40) REVERT: A 93 ASP cc_start: 0.8878 (p0) cc_final: 0.8635 (p0) REVERT: A 105 MET cc_start: 0.8562 (tpp) cc_final: 0.8152 (tpt) REVERT: A 120 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8262 (ttt-90) REVERT: A 314 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 370 MET cc_start: 0.8361 (mtt) cc_final: 0.8104 (mtt) REVERT: A 500 MET cc_start: 0.7784 (tpt) cc_final: 0.7063 (ptt) REVERT: B 23 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7186 (mtp85) REVERT: B 26 ASP cc_start: 0.8218 (t0) cc_final: 0.7886 (t0) REVERT: B 82 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7741 (mtt180) REVERT: B 171 GLU cc_start: 0.8006 (pt0) cc_final: 0.7761 (tp30) REVERT: C 23 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7231 (tmm-80) REVERT: C 67 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7741 (mmp80) REVERT: C 176 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7377 (mt0) REVERT: C 199 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8036 (pp20) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 1.7087 time to fit residues: 167.5700 Evaluate side-chains 93 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain B residue 164 SER 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 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3194 r_free = 0.3194 target = 0.112203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096125 restraints weight = 8644.472| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.65 r_work: 0.2932 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7290 Z= 0.132 Angle : 0.548 6.727 9896 Z= 0.280 Chirality : 0.041 0.131 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.426 115.397 1224 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.97 % Allowed : 17.35 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 929 helix: 1.22 (0.23), residues: 527 sheet: -0.72 (0.74), residues: 62 loop : -1.74 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.009 0.001 PHE C 19 TYR 0.016 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 331) hydrogen bonds : angle 3.35386 ( 978) covalent geometry : bond 0.00323 ( 7290) covalent geometry : angle 0.54824 ( 9896) ********************** 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 93 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8378 (mm110) cc_final: 0.8149 (mm-40) REVERT: A 93 ASP cc_start: 0.8877 (p0) cc_final: 0.8643 (p0) REVERT: A 105 MET cc_start: 0.8559 (tpp) cc_final: 0.8146 (tpt) REVERT: A 120 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8293 (ttt-90) REVERT: A 314 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 370 MET cc_start: 0.8347 (mtt) cc_final: 0.8103 (mtt) REVERT: A 500 MET cc_start: 0.7778 (tpt) cc_final: 0.7065 (ptt) REVERT: B 23 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7175 (mtp85) REVERT: B 26 ASP cc_start: 0.8199 (t0) cc_final: 0.7891 (t0) REVERT: B 82 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7744 (mtt180) REVERT: C 23 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7221 (tmm-80) REVERT: C 67 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7743 (mmp80) REVERT: C 176 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7390 (mt0) REVERT: C 199 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8053 (pp20) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 2.2052 time to fit residues: 200.6810 Evaluate side-chains 95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain B residue 164 SER 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 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3268 r_free = 0.3268 target = 0.117676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102119 restraints weight = 8307.872| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.59 r_work: 0.2963 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7290 Z= 0.121 Angle : 0.530 6.377 9896 Z= 0.272 Chirality : 0.040 0.125 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.272 114.614 1224 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.97 % Allowed : 17.49 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.28), residues: 929 helix: 1.32 (0.23), residues: 522 sheet: -0.68 (0.74), residues: 62 loop : -1.74 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.008 0.001 PHE A 360 TYR 0.018 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 331) hydrogen bonds : angle 3.31287 ( 978) covalent geometry : bond 0.00291 ( 7290) covalent geometry : angle 0.53028 ( 9896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.05 seconds wall clock time: 104 minutes 22.95 seconds (6262.95 seconds total)