Starting phenix.real_space_refine on Thu Nov 14 19:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_36797.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_36797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_36797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_36797.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1o_36797/11_2024/8k1o_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.57, per 1000 atoms: 0.78 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: 2.10 Conformation dependent library (CDL) restraints added in 861.3 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: 0.74 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: 2.00 Time building geometry restraints manager: 2.37 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: 3.430 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- 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= 0.441 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 *********************** 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 : 0.729 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: 1.5045 time to fit residues: 237.1325 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 : 0.809 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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= 0.249 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 *********************** 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 : 0.813 Fit side-chains REVERT: A 105 MET cc_start: 0.7922 (tpp) cc_final: 0.7547 (tpt) REVERT: A 120 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: A 128 SER cc_start: 0.7910 (m) cc_final: 0.7702 (p) REVERT: A 314 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 23 ARG cc_start: 0.7186 (mtt90) cc_final: 0.6921 (mtp85) REVERT: B 26 ASP cc_start: 0.7347 (m-30) cc_final: 0.6901 (t0) REVERT: C 67 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7238 (mmp80) REVERT: C 176 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7075 (mt0) REVERT: C 182 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.7062 (ttm170) REVERT: C 199 GLU cc_start: 0.7839 (pt0) cc_final: 0.7449 (pp20) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 1.3739 time to fit residues: 154.4043 Evaluate side-chains 100 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2159 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= 0.227 Angle : 0.587 8.823 9896 Z= 0.290 Chirality : 0.042 0.141 1167 Planarity : 0.004 0.040 1225 Dihedral : 14.026 122.728 1225 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.97 % Allowed : 13.96 % 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 (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: -0.76 (0.28), residues: 929 helix: 0.56 (0.23), residues: 540 sheet: -0.83 (0.67), residues: 70 loop : -2.27 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 44 HIS 0.008 0.001 HIS C 193 PHE 0.011 0.001 PHE C 40 TYR 0.011 0.001 TYR A 432 ARG 0.006 0.000 ARG A 67 *********************** 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 107 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.758 Fit side-chains REVERT: A 93 ASP cc_start: 0.8597 (p0) cc_final: 0.8384 (p0) REVERT: A 105 MET cc_start: 0.7940 (tpp) cc_final: 0.7539 (tpt) REVERT: A 120 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7998 (ttt-90) REVERT: A 314 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8221 (tp) REVERT: A 382 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7672 (mtp180) REVERT: B 23 ARG cc_start: 0.7219 (mtt90) cc_final: 0.7006 (mtp85) REVERT: B 26 ASP cc_start: 0.7346 (m-30) cc_final: 0.7048 (t0) REVERT: B 171 GLU cc_start: 0.7720 (pt0) cc_final: 0.7322 (tp30) REVERT: B 172 ASN cc_start: 0.8010 (t0) cc_final: 0.7757 (t0) REVERT: C 67 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7294 (mmp80) REVERT: C 176 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7020 (mt0) REVERT: C 199 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: C 212 LYS cc_start: 0.8675 (ptpp) cc_final: 0.8371 (ptpt) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 1.6090 time to fit residues: 171.4741 Evaluate side-chains 90 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2299 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= 0.193 Angle : 0.542 8.375 9896 Z= 0.272 Chirality : 0.041 0.136 1167 Planarity : 0.004 0.041 1225 Dihedral : 13.066 117.567 1224 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 14.95 % Favored : 83.22 % 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: -0.44 (0.28), residues: 929 helix: 0.79 (0.24), residues: 535 sheet: -0.67 (0.69), residues: 67 loop : -2.04 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 44 HIS 0.005 0.001 HIS C 193 PHE 0.009 0.001 PHE C 19 TYR 0.012 0.001 TYR A 432 ARG 0.007 0.000 ARG A 67 *********************** 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 98 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.740 Fit side-chains REVERT: A 93 ASP cc_start: 0.8693 (p0) cc_final: 0.8419 (p0) REVERT: A 105 MET cc_start: 0.7956 (tpp) cc_final: 0.7559 (tpt) REVERT: A 120 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8011 (ttt-90) REVERT: A 314 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 536 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7042 (tp) REVERT: B 23 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6954 (mtp85) REVERT: B 26 ASP cc_start: 0.7302 (m-30) cc_final: 0.7001 (t0) REVERT: B 171 GLU cc_start: 0.7688 (pt0) cc_final: 0.7366 (tp30) REVERT: B 172 ASN cc_start: 0.7941 (t0) cc_final: 0.7688 (t0) REVERT: C 23 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6940 (tmt90) REVERT: C 67 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7277 (mmp80) REVERT: C 176 GLN cc_start: 0.7613 (mm-40) cc_final: 0.6991 (mt0) REVERT: C 199 GLU cc_start: 0.7797 (pt0) cc_final: 0.7523 (pp20) REVERT: C 212 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8335 (ptpt) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 1.8090 time to fit residues: 175.7707 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 A residue 536 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 216 SER Chi-restraints excluded: chain C residue 23 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2392 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= 0.239 Angle : 0.572 9.106 9896 Z= 0.285 Chirality : 0.042 0.136 1167 Planarity : 0.004 0.041 1225 Dihedral : 12.967 118.931 1224 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.26 % Allowed : 16.08 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.28), residues: 929 helix: 0.83 (0.23), residues: 534 sheet: -0.97 (0.73), residues: 62 loop : -1.93 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 44 HIS 0.006 0.001 HIS C 193 PHE 0.011 0.001 PHE C 19 TYR 0.008 0.001 TYR A 56 ARG 0.007 0.000 ARG A 67 *********************** 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 96 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.775 Fit side-chains REVERT: A 93 ASP cc_start: 0.8612 (p0) cc_final: 0.8357 (p0) REVERT: A 105 MET cc_start: 0.7960 (tpp) cc_final: 0.7599 (tpt) REVERT: A 120 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8001 (ttt-90) REVERT: A 314 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (tp) REVERT: A 500 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6857 (ptt) REVERT: B 23 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6972 (mtp85) REVERT: B 26 ASP cc_start: 0.7289 (m-30) cc_final: 0.6992 (t0) REVERT: B 172 ASN cc_start: 0.7925 (t0) cc_final: 0.7721 (t0) REVERT: C 67 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7276 (mmp80) REVERT: C 176 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7051 (mt0) REVERT: C 199 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7565 (pp20) outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 1.6894 time to fit residues: 157.3536 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 A residue 500 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 B residue 216 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 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2492 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= 0.191 Angle : 0.525 8.364 9896 Z= 0.266 Chirality : 0.041 0.130 1167 Planarity : 0.004 0.042 1225 Dihedral : 12.566 114.938 1224 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.26 % Allowed : 15.80 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.28), residues: 929 helix: 1.02 (0.24), residues: 528 sheet: -0.85 (0.74), residues: 62 loop : -1.87 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.008 0.001 PHE C 19 TYR 0.014 0.001 TYR A 432 ARG 0.007 0.000 ARG A 67 *********************** 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 98 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8635 (p0) cc_final: 0.8406 (p0) REVERT: A 105 MET cc_start: 0.7941 (tpp) cc_final: 0.7567 (tpt) REVERT: A 120 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8014 (ttt-90) REVERT: A 314 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 370 MET cc_start: 0.7750 (mtt) cc_final: 0.7484 (mtt) REVERT: A 500 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6889 (ptt) REVERT: B 23 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6935 (mtp85) REVERT: B 26 ASP cc_start: 0.7297 (m-30) cc_final: 0.6996 (t0) REVERT: C 67 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7274 (mmp80) REVERT: C 176 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7045 (mt0) REVERT: C 199 GLU cc_start: 0.7810 (pt0) cc_final: 0.7439 (pp20) outliers start: 16 outliers final: 6 residues processed: 91 average time/residue: 1.6581 time to fit residues: 157.2577 Evaluate side-chains 86 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 A residue 500 MET 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 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2541 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= 0.241 Angle : 0.572 9.091 9896 Z= 0.287 Chirality : 0.042 0.135 1167 Planarity : 0.004 0.042 1225 Dihedral : 12.680 116.907 1224 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.82 % Allowed : 15.94 % Favored : 81.24 % 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: -0.20 (0.28), residues: 929 helix: 0.96 (0.23), residues: 534 sheet: -0.87 (0.74), residues: 62 loop : -1.81 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 44 HIS 0.006 0.001 HIS C 193 PHE 0.011 0.001 PHE C 19 TYR 0.007 0.001 TYR A 56 ARG 0.008 0.000 ARG A 67 *********************** 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 103 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8614 (t) cc_final: 0.8306 (m) REVERT: A 93 ASP cc_start: 0.8609 (p0) cc_final: 0.8364 (p0) REVERT: A 105 MET cc_start: 0.7940 (tpp) cc_final: 0.7560 (tpt) REVERT: A 120 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8003 (ttt-90) REVERT: A 286 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6926 (mp0) REVERT: A 314 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 500 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6794 (ptt) REVERT: B 23 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6959 (mtp85) REVERT: B 26 ASP cc_start: 0.7368 (m-30) cc_final: 0.7025 (t0) REVERT: B 172 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7351 (m-40) REVERT: C 67 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7273 (mmp80) REVERT: C 176 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7041 (mt0) REVERT: C 199 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7548 (pp20) outliers start: 20 outliers final: 9 residues processed: 95 average time/residue: 1.6514 time to fit residues: 163.7619 Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 500 MET 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 172 ASN 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 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 0.0470 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2595 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= 0.198 Angle : 0.533 8.491 9896 Z= 0.271 Chirality : 0.041 0.127 1167 Planarity : 0.004 0.043 1225 Dihedral : 12.445 114.886 1224 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: -0.03 (0.28), residues: 929 helix: 1.13 (0.23), residues: 528 sheet: -0.83 (0.74), residues: 62 loop : -1.73 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.008 0.001 PHE A 360 TYR 0.015 0.001 TYR A 432 ARG 0.007 0.000 ARG A 67 *********************** 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: 17 poor density : 83 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.8581 (t) cc_final: 0.8295 (m) REVERT: A 93 ASP cc_start: 0.8593 (p0) cc_final: 0.8375 (p0) REVERT: A 105 MET cc_start: 0.7951 (tpp) cc_final: 0.7563 (tpt) REVERT: A 120 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8020 (ttt-90) REVERT: A 286 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6947 (mp0) REVERT: A 314 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 370 MET cc_start: 0.7786 (mtt) cc_final: 0.7474 (mtt) REVERT: A 387 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: A 500 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6767 (ptm) REVERT: A 536 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7158 (tp) REVERT: B 23 ARG cc_start: 0.7253 (mtt90) cc_final: 0.6812 (mtp85) REVERT: B 172 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7300 (m-40) REVERT: C 176 GLN cc_start: 0.7603 (mm-40) cc_final: 0.6982 (mt0) REVERT: C 199 GLU cc_start: 0.7791 (pt0) cc_final: 0.7530 (pp20) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 1.7569 time to fit residues: 166.8041 Evaluate side-chains 94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 387 GLU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 536 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 172 ASN Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 23 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2673 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= 0.182 Angle : 0.521 8.124 9896 Z= 0.267 Chirality : 0.040 0.125 1167 Planarity : 0.004 0.042 1225 Dihedral : 12.196 113.654 1224 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.40 % Allowed : 16.78 % 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: 0.14 (0.28), residues: 929 helix: 1.28 (0.23), residues: 528 sheet: -0.72 (0.74), residues: 62 loop : -1.67 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.008 0.001 PHE A 360 TYR 0.017 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 *********************** 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 : 0.753 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8482 (t) cc_final: 0.8211 (m) REVERT: A 105 MET cc_start: 0.7923 (tpp) cc_final: 0.7542 (tpt) REVERT: A 120 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8028 (ttt-90) REVERT: A 286 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6944 (mp0) REVERT: A 314 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 370 MET cc_start: 0.7706 (mtt) cc_final: 0.7409 (mtt) REVERT: A 500 MET cc_start: 0.7173 (tpt) cc_final: 0.6759 (ptt) REVERT: A 536 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7083 (tp) REVERT: B 23 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6890 (mtp85) REVERT: B 82 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7167 (mtt180) REVERT: B 172 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7305 (m-40) REVERT: C 23 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6848 (ttp80) REVERT: C 176 GLN cc_start: 0.7594 (mm-40) cc_final: 0.6983 (mt0) REVERT: C 199 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7588 (pp20) outliers start: 17 outliers final: 7 residues processed: 93 average time/residue: 1.6754 time to fit residues: 162.6154 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 536 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 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 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7290 Z= 0.167 Angle : 0.503 5.729 9896 Z= 0.261 Chirality : 0.040 0.126 1167 Planarity : 0.004 0.042 1225 Dihedral : 11.954 112.789 1224 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.55 % Allowed : 17.77 % 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: 0.33 (0.28), residues: 929 helix: 1.49 (0.24), residues: 528 sheet: -0.66 (0.75), residues: 62 loop : -1.70 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 44 HIS 0.002 0.001 HIS A 384 PHE 0.007 0.001 PHE A 360 TYR 0.007 0.001 TYR A 489 ARG 0.008 0.000 ARG A 67 ********************** 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: 11 poor density : 82 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.7926 (tpp) cc_final: 0.7539 (tpt) REVERT: A 120 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8032 (ttt-90) REVERT: A 286 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6961 (mp0) REVERT: A 314 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 370 MET cc_start: 0.7655 (mtt) cc_final: 0.7362 (mtt) REVERT: A 500 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6795 (ptt) REVERT: B 23 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6885 (mtp85) REVERT: B 26 ASP cc_start: 0.7379 (t70) cc_final: 0.7103 (t70) REVERT: B 82 ARG cc_start: 0.7584 (ptp90) cc_final: 0.7187 (mtt180) REVERT: B 172 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7298 (m-40) REVERT: C 23 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6791 (ttp80) REVERT: C 176 GLN cc_start: 0.7587 (mm-40) cc_final: 0.6982 (mt0) REVERT: C 199 GLU cc_start: 0.7805 (pt0) cc_final: 0.7532 (pp20) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 1.3496 time to fit residues: 122.8310 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 : 0.764 ------------------------------------------------------------------------------- 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 500 MET 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 172 ASN Chi-restraints excluded: chain C residue 23 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3293 r_free = 0.3293 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104080 restraints weight = 8157.893| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.64 r_work: 0.2989 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2780 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= 0.170 Angle : 0.510 6.099 9896 Z= 0.263 Chirality : 0.040 0.132 1167 Planarity : 0.004 0.042 1225 Dihedral : 11.853 113.009 1224 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.55 % Allowed : 18.34 % Favored : 80.11 % 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: 0.55 (0.28), residues: 929 helix: 1.64 (0.24), residues: 522 sheet: 0.11 (0.80), residues: 52 loop : -1.59 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 44 HIS 0.004 0.001 HIS C 193 PHE 0.007 0.001 PHE A 360 TYR 0.019 0.001 TYR A 432 ARG 0.008 0.000 ARG A 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.42 seconds wall clock time: 64 minutes 14.21 seconds (3854.21 seconds total)