Starting phenix.real_space_refine on Tue Aug 4 21:58:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4x_53571/08_2026/9r4x_53571.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 5 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 4254 2.51 5 N 1146 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6762 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3318 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3321 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.22 Number of scatterers: 6762 At special positions: 0 Unit cell: (73.623, 73.623, 110.968, 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 55 16.00 P 5 15.00 Mg 1 11.99 O 1301 8.00 N 1146 7.00 C 4254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 385.9 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 52.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.648A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.693A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.381A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.592A pdb=" N ASN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.564A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.881A pdb=" N SER A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.186A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.731A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.715A pdb=" N MET A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.896A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.556A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.300A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.846A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.089A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.662A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.859A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.721A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.853A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.158A pdb=" N MET B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.769A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.945A pdb=" N ILE A 93 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL A 66 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS A 171 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER A 139 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.996A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN B 8 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU B 3 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLU B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B 133 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 354 removed outlier: 6.138A pdb=" N ALA B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N SER B 352 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA B 315 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 364 " --> pdb=" O ARG B 318 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 873 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: 1.08 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1221 1.32 - 1.44: 1791 1.44 - 1.57: 3804 1.57 - 1.69: 12 1.69 - 1.81: 87 Bond restraints: 6915 Sorted by residual: bond pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.37e+00 bond pdb=" CA PRO A 359 " pdb=" C PRO A 359 " ideal model delta sigma weight residual 1.517 1.525 -0.008 6.70e-03 2.23e+04 1.35e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" CB GLN A 256 " pdb=" CG GLN A 256 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 bond pdb=" CG GLN A 256 " pdb=" CD GLN A 256 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.85e-01 ... (remaining 6910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 9142 1.20 - 2.40: 179 2.40 - 3.60: 49 3.60 - 4.80: 13 4.80 - 6.00: 7 Bond angle restraints: 9390 Sorted by residual: angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 105.00 6.00 3.00e+00 1.11e-01 4.00e+00 angle pdb=" C20 TA1 B 502 " pdb=" C21 TA1 B 502 " pdb=" C24 TA1 B 502 " ideal model delta sigma weight residual 107.07 112.59 -5.52 3.00e+00 1.11e-01 3.39e+00 angle pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 111.00 105.57 5.43 3.00e+00 1.11e-01 3.28e+00 angle pdb=" C4' GDP B 501 " pdb=" C3' GDP B 501 " pdb=" C2' GDP B 501 " ideal model delta sigma weight residual 111.00 105.64 5.36 3.00e+00 1.11e-01 3.20e+00 angle pdb=" C3' GDP B 501 " pdb=" C2' GDP B 501 " pdb=" C1' GDP B 501 " ideal model delta sigma weight residual 111.00 106.01 4.99 3.00e+00 1.11e-01 2.77e+00 ... (remaining 9385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 4100 34.25 - 68.49: 51 68.49 - 102.74: 15 102.74 - 136.98: 11 136.98 - 171.23: 6 Dihedral angle restraints: 4183 sinusoidal: 1738 harmonic: 2445 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.63 171.23 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 177.30 -16.98 -165.72 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 141.85 119.02 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 4180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 688 0.033 - 0.067: 232 0.067 - 0.100: 73 0.100 - 0.133: 31 0.133 - 0.167: 1 Chirality restraints: 1025 Sorted by residual: chirality pdb=" C10 TA1 B 502 " pdb=" C02 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" C18 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.54 2.38 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 378 " pdb=" N ILE A 378 " pdb=" C ILE A 378 " pdb=" CB ILE A 378 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1022 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 86 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 87 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 31 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 32 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 260 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 261 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.014 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 53 2.58 - 3.16: 5669 3.16 - 3.74: 10990 3.74 - 4.32: 15220 4.32 - 4.90: 25557 Nonbonded interactions: 57489 Sorted by model distance: nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.006 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.049 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 2.066 2.170 nonbonded pdb=" O ILE B 210 " pdb=" OG1 THR B 214 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 27 " pdb=" OG SER A 236 " model vdw 2.219 3.040 ... (remaining 57484 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.002 0.031 6915 Z= 0.098 Angle : 0.480 6.001 9390 Z= 0.234 Chirality : 0.040 0.167 1025 Planarity : 0.003 0.053 1217 Dihedral : 16.270 171.225 2613 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.66 % Allowed : 4.16 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.30), residues: 842 helix: 1.74 (0.28), residues: 365 sheet: -0.55 (0.46), residues: 142 loop : -0.77 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.008 0.001 TYR B 310 PHE 0.006 0.001 PHE B 394 TRP 0.011 0.002 TRP B 397 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 6915) covalent geometry : angle 0.48008 / 0.23 ( 9390) hydrogen bonds : bond 0.17074 / 11.44 ( 305) hydrogen bonds : angle 6.32560 / 4.50 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.269 Fit side-chains REVERT: A 217 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 137 HIS cc_start: 0.7789 (t-170) cc_final: 0.7497 (t-170) REVERT: B 215 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 267 MET cc_start: 0.8174 (mtp) cc_final: 0.7961 (mtt) REVERT: B 397 TRP cc_start: 0.7035 (m100) cc_final: 0.6753 (m-10) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 0.0815 time to fit residues: 10.9010 Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 300 ASN B 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.101901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.087083 restraints weight = 12476.067| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.57 r_work: 0.3577 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6915 Z= 0.101 Angle : 0.545 9.645 9390 Z= 0.257 Chirality : 0.042 0.283 1025 Planarity : 0.004 0.038 1217 Dihedral : 15.786 169.063 1061 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 7.63 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 842 helix: 1.59 (0.27), residues: 376 sheet: -1.00 (0.44), residues: 133 loop : -0.57 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.013 0.001 TYR B 51 PHE 0.014 0.001 PHE A 149 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6915) covalent geometry : angle 0.54502 / 0.26 ( 9390) hydrogen bonds : bond 0.03439 / 2.36 ( 305) hydrogen bonds : angle 4.54677 / 3.27 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.185 Fit side-chains REVERT: A 217 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 211 CYS cc_start: 0.7445 (m) cc_final: 0.7241 (m) REVERT: B 215 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 397 TRP cc_start: 0.7555 (m100) cc_final: 0.7122 (m-10) REVERT: B 414 ASN cc_start: 0.7125 (m-40) cc_final: 0.6640 (t0) REVERT: B 415 MET cc_start: 0.7374 (tpp) cc_final: 0.7163 (tpp) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.0680 time to fit residues: 7.2247 Evaluate side-chains 63 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.095836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081001 restraints weight = 12876.354| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.56 r_work: 0.3467 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6915 Z= 0.223 Angle : 0.634 8.485 9390 Z= 0.306 Chirality : 0.048 0.468 1025 Planarity : 0.004 0.038 1217 Dihedral : 13.041 168.871 1058 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.64 % Allowed : 8.60 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.30), residues: 842 helix: 1.03 (0.27), residues: 379 sheet: -1.18 (0.46), residues: 125 loop : -0.77 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.014 0.002 TYR B 310 PHE 0.018 0.002 PHE B 394 TRP 0.013 0.002 TRP A 21 HIS 0.005 0.002 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 6915) covalent geometry : angle 0.63430 / 0.31 ( 9390) hydrogen bonds : bond 0.04390 / 2.95 ( 305) hydrogen bonds : angle 4.59134 / 3.32 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.259 Fit side-chains REVERT: A 217 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 211 CYS cc_start: 0.7702 (m) cc_final: 0.7462 (m) REVERT: B 321 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6070 (ptm) REVERT: B 414 ASN cc_start: 0.7101 (m-40) cc_final: 0.6615 (t0) outliers start: 19 outliers final: 13 residues processed: 68 average time/residue: 0.0635 time to fit residues: 6.4826 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082754 restraints weight = 12757.190| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.60 r_work: 0.3495 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6915 Z= 0.136 Angle : 0.563 8.427 9390 Z= 0.267 Chirality : 0.044 0.371 1025 Planarity : 0.004 0.042 1217 Dihedral : 12.232 168.849 1056 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 9.29 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.30), residues: 842 helix: 1.28 (0.27), residues: 379 sheet: -1.16 (0.46), residues: 125 loop : -0.70 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 310 PHE 0.012 0.001 PHE A 138 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6915) covalent geometry : angle 0.56284 / 0.27 ( 9390) hydrogen bonds : bond 0.03541 / 2.39 ( 305) hydrogen bonds : angle 4.29366 / 3.11 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.306 Fit side-chains REVERT: A 217 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 279 GLU cc_start: 0.7708 (mp0) cc_final: 0.7298 (mp0) REVERT: A 301 MET cc_start: 0.7693 (mmt) cc_final: 0.7180 (mmp) REVERT: B 211 CYS cc_start: 0.7629 (m) cc_final: 0.7393 (m) REVERT: B 414 ASN cc_start: 0.7081 (m-40) cc_final: 0.6622 (t0) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.0641 time to fit residues: 6.0734 Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.0970 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 58 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.9615 > 50:) chunk 46 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.097289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082384 restraints weight = 12878.852| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.62 r_work: 0.3487 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6915 Z= 0.150 Angle : 0.570 8.090 9390 Z= 0.272 Chirality : 0.044 0.279 1025 Planarity : 0.004 0.042 1217 Dihedral : 12.115 168.805 1056 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.91 % Allowed : 9.29 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 842 helix: 1.28 (0.27), residues: 379 sheet: -1.29 (0.45), residues: 125 loop : -0.72 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.011 0.001 TYR B 310 PHE 0.011 0.001 PHE B 394 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6915) covalent geometry : angle 0.57049 / 0.27 ( 9390) hydrogen bonds : bond 0.03599 / 2.42 ( 305) hydrogen bonds : angle 4.21644 / 3.07 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.274 Fit side-chains REVERT: A 217 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 279 GLU cc_start: 0.7723 (mp0) cc_final: 0.7309 (mp0) REVERT: A 301 MET cc_start: 0.7722 (mmt) cc_final: 0.7244 (mmp) REVERT: B 211 CYS cc_start: 0.7637 (m) cc_final: 0.7402 (m) REVERT: B 321 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6968 (ptm) REVERT: B 414 ASN cc_start: 0.7062 (m-40) cc_final: 0.6612 (t0) outliers start: 21 outliers final: 15 residues processed: 71 average time/residue: 0.0717 time to fit residues: 7.4167 Evaluate side-chains 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 0.0570 chunk 58 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 298 ASN B 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.099037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.084203 restraints weight = 12803.013| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.62 r_work: 0.3523 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6915 Z= 0.106 Angle : 0.530 9.276 9390 Z= 0.252 Chirality : 0.042 0.224 1025 Planarity : 0.004 0.043 1217 Dihedral : 11.873 168.555 1056 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 10.26 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.30), residues: 842 helix: 1.51 (0.28), residues: 379 sheet: -1.22 (0.45), residues: 125 loop : -0.64 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.009 0.001 TYR B 310 PHE 0.009 0.001 PHE A 138 TRP 0.014 0.001 TRP A 21 HIS 0.002 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6915) covalent geometry : angle 0.52984 / 0.25 ( 9390) hydrogen bonds : bond 0.03167 / 2.14 ( 305) hydrogen bonds : angle 4.01695 / 2.92 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.316 Fit side-chains REVERT: A 217 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 432 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.4785 (t80) REVERT: B 211 CYS cc_start: 0.7557 (m) cc_final: 0.7330 (m) REVERT: B 321 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6942 (ptm) REVERT: B 414 ASN cc_start: 0.7044 (m-40) cc_final: 0.6619 (t0) outliers start: 17 outliers final: 9 residues processed: 72 average time/residue: 0.0719 time to fit residues: 7.5726 Evaluate side-chains 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 0.0170 chunk 36 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 2.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083090 restraints weight = 12724.438| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.58 r_work: 0.3504 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6915 Z= 0.140 Angle : 0.567 9.305 9390 Z= 0.270 Chirality : 0.043 0.217 1025 Planarity : 0.004 0.042 1217 Dihedral : 11.793 168.487 1056 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.05 % Allowed : 10.96 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.30), residues: 842 helix: 1.38 (0.27), residues: 380 sheet: -1.28 (0.45), residues: 125 loop : -0.68 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR B 310 PHE 0.010 0.001 PHE B 394 TRP 0.014 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6915) covalent geometry : angle 0.56677 / 0.27 ( 9390) hydrogen bonds : bond 0.03467 / 2.32 ( 305) hydrogen bonds : angle 4.07546 / 2.96 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.313 Fit side-chains REVERT: A 217 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 432 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.4806 (t80) REVERT: B 211 CYS cc_start: 0.7682 (m) cc_final: 0.7467 (m) REVERT: B 321 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7026 (ptm) REVERT: B 414 ASN cc_start: 0.7179 (m-40) cc_final: 0.6746 (t0) REVERT: B 422 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.5905 (t80) outliers start: 22 outliers final: 14 residues processed: 71 average time/residue: 0.0791 time to fit residues: 8.0595 Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.097851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083156 restraints weight = 12784.179| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.57 r_work: 0.3507 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6915 Z= 0.139 Angle : 0.564 8.655 9390 Z= 0.271 Chirality : 0.043 0.210 1025 Planarity : 0.004 0.042 1217 Dihedral : 11.702 168.407 1056 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.77 % Allowed : 11.51 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 842 helix: 1.37 (0.27), residues: 380 sheet: -1.29 (0.45), residues: 125 loop : -0.70 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR B 310 PHE 0.010 0.001 PHE A 395 TRP 0.014 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6915) covalent geometry : angle 0.56375 / 0.27 ( 9390) hydrogen bonds : bond 0.03430 / 2.31 ( 305) hydrogen bonds : angle 4.07527 / 2.97 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.262 Fit side-chains REVERT: A 217 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 432 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.4789 (t80) REVERT: B 211 CYS cc_start: 0.7795 (m) cc_final: 0.7558 (m) REVERT: B 321 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7000 (ptm) REVERT: B 422 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.5877 (t80) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.0710 time to fit residues: 7.2124 Evaluate side-chains 70 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.095880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081006 restraints weight = 12957.714| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.58 r_work: 0.3466 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6915 Z= 0.204 Angle : 0.621 9.545 9390 Z= 0.301 Chirality : 0.045 0.217 1025 Planarity : 0.004 0.042 1217 Dihedral : 11.769 168.162 1056 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.91 % Allowed : 11.79 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.30), residues: 842 helix: 1.06 (0.27), residues: 380 sheet: -1.35 (0.47), residues: 119 loop : -0.82 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.014 0.002 TYR B 310 PHE 0.014 0.002 PHE B 394 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 6915) covalent geometry : angle 0.62062 / 0.30 ( 9390) hydrogen bonds : bond 0.03998 / 2.69 ( 305) hydrogen bonds : angle 4.31666 / 3.14 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.259 Fit side-chains REVERT: A 217 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 432 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.4694 (t80) REVERT: B 66 MET cc_start: 0.6940 (tmm) cc_final: 0.6684 (ttp) REVERT: B 321 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7186 (ptm) REVERT: B 406 MET cc_start: 0.7378 (pmm) cc_final: 0.7167 (pmm) REVERT: B 422 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.5883 (t80) outliers start: 21 outliers final: 16 residues processed: 69 average time/residue: 0.0745 time to fit residues: 7.4934 Evaluate side-chains 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.095922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081134 restraints weight = 12832.363| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.55 r_work: 0.3473 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6915 Z= 0.194 Angle : 0.610 9.574 9390 Z= 0.296 Chirality : 0.045 0.212 1025 Planarity : 0.004 0.042 1217 Dihedral : 11.743 168.006 1056 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.05 % Allowed : 11.65 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.30), residues: 842 helix: 0.99 (0.27), residues: 380 sheet: -1.48 (0.47), residues: 119 loop : -0.88 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.012 0.001 TYR B 310 PHE 0.013 0.002 PHE A 395 TRP 0.014 0.002 TRP A 21 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 6915) covalent geometry : angle 0.60998 / 0.30 ( 9390) hydrogen bonds : bond 0.03879 / 2.62 ( 305) hydrogen bonds : angle 4.33928 / 3.17 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.253 Fit side-chains REVERT: A 217 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 432 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.4654 (t80) REVERT: B 321 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7236 (ptm) REVERT: B 422 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.5865 (t80) outliers start: 22 outliers final: 16 residues processed: 68 average time/residue: 0.0789 time to fit residues: 7.7232 Evaluate side-chains 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082258 restraints weight = 12710.153| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.58 r_work: 0.3493 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6915 Z= 0.148 Angle : 0.578 9.606 9390 Z= 0.277 Chirality : 0.043 0.207 1025 Planarity : 0.004 0.042 1217 Dihedral : 11.610 167.920 1056 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.91 % Allowed : 11.93 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.30), residues: 842 helix: 1.16 (0.27), residues: 380 sheet: -1.39 (0.47), residues: 119 loop : -0.84 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR B 310 PHE 0.011 0.001 PHE A 395 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6915) covalent geometry : angle 0.57810 / 0.28 ( 9390) hydrogen bonds : bond 0.03531 / 2.39 ( 305) hydrogen bonds : angle 4.21039 / 3.08 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1791.14 seconds wall clock time: 31 minutes 34.99 seconds (1894.99 seconds total)