Starting phenix.real_space_refine on Thu Jul 2 04:31:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.map" model { file = "/net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g3g_50998/07_2026/9g3g_50998.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.144 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 4358 2.51 5 N 1026 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6482 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3184 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.63, per 1000 atoms: 0.25 Number of scatterers: 6482 At special positions: 0 Unit cell: (93.002, 65.408, 100.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 2 15.00 O 1076 8.00 N 1026 7.00 C 4358 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: 0.45 Conformation dependent library (CDL) restraints added in 343.9 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 90.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.516A pdb=" N PHE A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.651A pdb=" N ARG A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 54 through 79 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 125 removed outlier: 4.288A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 130 through 177 removed outlier: 3.880A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 227 removed outlier: 3.538A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 262 removed outlier: 3.525A pdb=" N ILE A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 287 removed outlier: 4.456A pdb=" N GLY A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 337 removed outlier: 3.926A pdb=" N GLU A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.669A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 394 removed outlier: 3.557A pdb=" N LEU A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.573A pdb=" N PHE B 13 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.659A pdb=" N ARG B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 53' Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.522A pdb=" N SER B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 125 removed outlier: 4.270A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 130 through 177 removed outlier: 3.915A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 227 removed outlier: 4.366A pdb=" N THR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 262 Processing helix chain 'B' and resid 263 through 289 removed outlier: 4.428A pdb=" N GLY B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 337 removed outlier: 3.896A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.769A pdb=" N LEU B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 392 removed outlier: 3.894A pdb=" N GLU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 537 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.61 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: 1000 1.32 - 1.44: 2038 1.44 - 1.56: 3606 1.56 - 1.68: 4 1.68 - 1.80: 38 Bond restraints: 6686 Sorted by residual: bond pdb=" CA ILE A 239 " pdb=" CB ILE A 239 " ideal model delta sigma weight residual 1.537 1.550 -0.013 1.29e-02 6.01e+03 1.02e+00 bond pdb=" CA ILE A 239 " pdb=" C ILE A 239 " ideal model delta sigma weight residual 1.524 1.515 0.009 1.05e-02 9.07e+03 7.66e-01 bond pdb=" C ALA A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.57e-01 bond pdb=" CB GLN A 179 " pdb=" CG GLN A 179 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.39e-01 bond pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 1.465 1.478 -0.013 2.03e-02 2.43e+03 4.21e-01 ... (remaining 6681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8989 1.39 - 2.78: 86 2.78 - 4.17: 13 4.17 - 5.56: 8 5.56 - 6.95: 4 Bond angle restraints: 9100 Sorted by residual: angle pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " pdb=" CG LEU B 376 " ideal model delta sigma weight residual 116.30 123.25 -6.95 3.50e+00 8.16e-02 3.95e+00 angle pdb=" N ILE B 235 " pdb=" CA ILE B 235 " pdb=" C ILE B 235 " ideal model delta sigma weight residual 109.34 113.46 -4.12 2.08e+00 2.31e-01 3.92e+00 angle pdb=" CA PRO A 295 " pdb=" C PRO A 295 " pdb=" N PRO A 296 " ideal model delta sigma weight residual 117.93 120.27 -2.34 1.20e+00 6.94e-01 3.80e+00 angle pdb=" N PRO A 295 " pdb=" CA PRO A 295 " pdb=" C PRO A 295 " ideal model delta sigma weight residual 110.70 113.05 -2.35 1.22e+00 6.72e-01 3.71e+00 angle pdb=" C HIS B 391 " pdb=" N GLU B 392 " pdb=" CA GLU B 392 " ideal model delta sigma weight residual 121.70 125.16 -3.46 1.80e+00 3.09e-01 3.70e+00 ... (remaining 9095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 3303 15.96 - 31.92: 365 31.92 - 47.87: 78 47.87 - 63.83: 24 63.83 - 79.79: 2 Dihedral angle restraints: 3772 sinusoidal: 1480 harmonic: 2292 Sorted by residual: dihedral pdb=" CA ALA B 293 " pdb=" C ALA B 293 " pdb=" N THR B 294 " pdb=" CA THR B 294 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG B 311 " pdb=" CD ARG B 311 " pdb=" NE ARG B 311 " pdb=" CZ ARG B 311 " ideal model delta sinusoidal sigma weight residual 180.00 135.87 44.13 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 311 " pdb=" CD ARG A 311 " pdb=" NE ARG A 311 " pdb=" CZ ARG A 311 " ideal model delta sinusoidal sigma weight residual 180.00 137.72 42.28 2 1.50e+01 4.44e-03 9.66e+00 ... (remaining 3769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 670 0.027 - 0.055: 197 0.055 - 0.082: 98 0.082 - 0.110: 28 0.110 - 0.137: 10 Chirality restraints: 1003 Sorted by residual: chirality pdb=" CG LEU B 376 " pdb=" CB LEU B 376 " pdb=" CD1 LEU B 376 " pdb=" CD2 LEU B 376 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 239 " pdb=" N ILE A 239 " pdb=" C ILE A 239 " pdb=" CB ILE A 239 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1000 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 125 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 126 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 295 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 296 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 294 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 295 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.020 5.00e-02 4.00e+02 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1272 2.77 - 3.30: 6393 3.30 - 3.84: 10706 3.84 - 4.37: 12864 4.37 - 4.90: 22730 Nonbonded interactions: 53965 Sorted by model distance: nonbonded pdb=" OH TYR B 174 " pdb=" OE2 GLU B 390 " model vdw 2.238 3.040 nonbonded pdb=" NZ LYS A 281 " pdb=" OH TYR A 285 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP B 289 " pdb=" OG1 THR B 291 " model vdw 2.287 3.040 nonbonded pdb=" NZ LYS B 281 " pdb=" OH TYR B 285 " model vdw 2.316 3.120 nonbonded pdb=" O SER B 87 " pdb=" OG1 THR B 91 " model vdw 2.350 3.040 ... (remaining 53960 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 'A' and (resid 2 through 392 or resid 501)) selection = chain 'B' } 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: 0.930 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 0.023 6686 Z= 0.091 Angle : 0.406 6.952 9100 Z= 0.218 Chirality : 0.036 0.137 1003 Planarity : 0.004 0.076 1107 Dihedral : 14.078 79.789 2304 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.28), residues: 780 helix: 1.49 (0.19), residues: 651 sheet: None (None), residues: 0 loop : -1.07 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.007 0.001 TYR A 316 PHE 0.013 0.001 PHE A 389 TRP 0.011 0.001 TRP A 34 HIS 0.001 0.000 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 6686) covalent geometry : angle 0.40636 / 0.22 ( 9100) hydrogen bonds : bond 0.20840 / 13.77 ( 537) hydrogen bonds : angle 7.09534 / 5.48 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.277 Fit side-chains REVERT: B 253 MET cc_start: 0.6898 (ttp) cc_final: 0.5934 (mtt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0778 time to fit residues: 10.3735 Evaluate side-chains 85 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104304 restraints weight = 6958.575| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.30 r_work: 0.2863 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6686 Z= 0.205 Angle : 0.514 6.669 9100 Z= 0.276 Chirality : 0.042 0.134 1003 Planarity : 0.005 0.055 1107 Dihedral : 6.912 59.281 924 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 4.68 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.28), residues: 780 helix: 2.07 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -1.13 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.008 0.001 TYR A 383 PHE 0.019 0.002 PHE A 389 TRP 0.022 0.001 TRP A 34 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 6686) covalent geometry : angle 0.51408 / 0.28 ( 9100) hydrogen bonds : bond 0.05949 / 4.01 ( 537) hydrogen bonds : angle 4.56320 / 3.52 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.143 Fit side-chains REVERT: A 376 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7881 (tp) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.0739 time to fit residues: 8.9681 Evaluate side-chains 87 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.110559 restraints weight = 6895.871| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.25 r_work: 0.2938 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6686 Z= 0.118 Angle : 0.441 6.937 9100 Z= 0.233 Chirality : 0.038 0.128 1003 Planarity : 0.004 0.047 1107 Dihedral : 6.220 56.641 924 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 6.19 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.28), residues: 780 helix: 2.35 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.007 0.001 TYR B 116 PHE 0.014 0.001 PHE A 26 TRP 0.017 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 6686) covalent geometry : angle 0.44136 / 0.23 ( 9100) hydrogen bonds : bond 0.04690 / 3.16 ( 537) hydrogen bonds : angle 4.04469 / 3.11 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.150 Fit side-chains REVERT: B 197 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8304 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.0806 time to fit residues: 10.3183 Evaluate side-chains 85 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.134377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107424 restraints weight = 6933.386| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.31 r_work: 0.2923 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6686 Z= 0.129 Angle : 0.452 7.073 9100 Z= 0.237 Chirality : 0.039 0.171 1003 Planarity : 0.004 0.045 1107 Dihedral : 6.157 52.992 924 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.76 % Allowed : 7.85 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.28), residues: 780 helix: 2.40 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.97 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 82 TYR 0.009 0.001 TYR B 116 PHE 0.013 0.001 PHE A 164 TRP 0.016 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6686) covalent geometry : angle 0.45242 / 0.24 ( 9100) hydrogen bonds : bond 0.04650 / 3.13 ( 537) hydrogen bonds : angle 3.94505 / 3.02 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.157 Fit side-chains REVERT: A 376 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 276 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 299 ARG cc_start: 0.7374 (ttm170) cc_final: 0.7163 (ttm110) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.0796 time to fit residues: 9.3903 Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.133357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.106294 restraints weight = 6988.954| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.32 r_work: 0.2936 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6686 Z= 0.143 Angle : 0.459 6.776 9100 Z= 0.241 Chirality : 0.039 0.172 1003 Planarity : 0.004 0.045 1107 Dihedral : 6.242 51.085 924 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.21 % Allowed : 8.01 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.86 (0.28), residues: 780 helix: 2.38 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.024 0.001 PHE A 26 TRP 0.019 0.001 TRP B 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6686) covalent geometry : angle 0.45928 / 0.24 ( 9100) hydrogen bonds : bond 0.04775 / 3.22 ( 537) hydrogen bonds : angle 3.96095 / 3.03 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.175 Fit side-chains REVERT: A 376 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7883 (tp) REVERT: B 276 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8167 (mm-30) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.0807 time to fit residues: 9.9683 Evaluate side-chains 86 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107262 restraints weight = 6955.256| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.30 r_work: 0.2979 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6686 Z= 0.128 Angle : 0.457 7.357 9100 Z= 0.240 Chirality : 0.039 0.176 1003 Planarity : 0.004 0.045 1107 Dihedral : 6.047 50.148 924 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.91 % Allowed : 9.37 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.28), residues: 780 helix: 2.43 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.010 0.001 TYR A 316 PHE 0.019 0.001 PHE B 26 TRP 0.019 0.001 TRP B 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6686) covalent geometry : angle 0.45682 / 0.24 ( 9100) hydrogen bonds : bond 0.04603 / 3.09 ( 537) hydrogen bonds : angle 3.89701 / 2.98 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.224 Fit side-chains REVERT: A 376 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 276 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8117 (mm-30) REVERT: B 317 MET cc_start: 0.9119 (ttp) cc_final: 0.8708 (ttt) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.0751 time to fit residues: 9.1877 Evaluate side-chains 89 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.106493 restraints weight = 6960.698| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.24 r_work: 0.2908 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6686 Z= 0.153 Angle : 0.474 6.905 9100 Z= 0.249 Chirality : 0.040 0.178 1003 Planarity : 0.004 0.045 1107 Dihedral : 6.267 49.621 924 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.06 % Allowed : 9.21 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.28), residues: 780 helix: 2.35 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.017 0.001 PHE B 26 TRP 0.019 0.001 TRP A 34 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6686) covalent geometry : angle 0.47358 / 0.25 ( 9100) hydrogen bonds : bond 0.04854 / 3.27 ( 537) hydrogen bonds : angle 3.97003 / 3.03 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.254 Fit side-chains REVERT: A 376 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7921 (tp) REVERT: B 276 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8245 (mm-30) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.0853 time to fit residues: 10.4202 Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106870 restraints weight = 6878.860| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.25 r_work: 0.2911 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6686 Z= 0.140 Angle : 0.469 9.399 9100 Z= 0.245 Chirality : 0.039 0.235 1003 Planarity : 0.004 0.045 1107 Dihedral : 6.132 49.097 924 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.21 % Allowed : 9.21 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.28), residues: 780 helix: 2.38 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.016 0.001 PHE B 26 TRP 0.020 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6686) covalent geometry : angle 0.46876 / 0.25 ( 9100) hydrogen bonds : bond 0.04719 / 3.18 ( 537) hydrogen bonds : angle 3.93663 / 3.01 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.234 Fit side-chains REVERT: A 177 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 376 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 276 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8240 (mm-30) REVERT: B 317 MET cc_start: 0.9159 (ttp) cc_final: 0.8754 (ttt) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.0850 time to fit residues: 9.8337 Evaluate side-chains 87 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.105846 restraints weight = 6985.592| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.27 r_work: 0.2902 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6686 Z= 0.154 Angle : 0.478 7.853 9100 Z= 0.251 Chirality : 0.040 0.212 1003 Planarity : 0.004 0.044 1107 Dihedral : 6.273 48.453 924 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.21 % Allowed : 9.21 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.28), residues: 780 helix: 2.36 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.98 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.016 0.001 PHE B 26 TRP 0.021 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6686) covalent geometry : angle 0.47821 / 0.25 ( 9100) hydrogen bonds : bond 0.04867 / 3.28 ( 537) hydrogen bonds : angle 3.98207 / 3.04 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.223 Fit side-chains REVERT: A 177 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 376 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7908 (tp) REVERT: B 276 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8248 (mm-30) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.0749 time to fit residues: 8.6498 Evaluate side-chains 86 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.133626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107245 restraints weight = 6918.429| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.25 r_work: 0.2979 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6686 Z= 0.140 Angle : 0.474 10.420 9100 Z= 0.246 Chirality : 0.040 0.267 1003 Planarity : 0.004 0.044 1107 Dihedral : 6.105 47.804 924 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.06 % Allowed : 9.37 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.28), residues: 780 helix: 2.42 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.96 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.016 0.001 PHE B 26 TRP 0.021 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6686) covalent geometry : angle 0.47380 / 0.25 ( 9100) hydrogen bonds : bond 0.04696 / 3.16 ( 537) hydrogen bonds : angle 3.93535 / 3.01 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.231 Fit side-chains REVERT: A 177 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8253 (p0) REVERT: A 376 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7885 (tp) REVERT: B 276 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8205 (mm-30) REVERT: B 317 MET cc_start: 0.9148 (ttp) cc_final: 0.8734 (ttt) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.0731 time to fit residues: 8.5376 Evaluate side-chains 88 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.0030 chunk 53 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 0.0370 chunk 55 optimal weight: 0.9980 overall best weight: 0.2868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120088 restraints weight = 6815.516| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.28 r_work: 0.2986 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6686 Z= 0.105 Angle : 0.439 8.905 9100 Z= 0.228 Chirality : 0.038 0.211 1003 Planarity : 0.003 0.045 1107 Dihedral : 5.357 45.966 924 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.76 % Allowed : 9.82 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.28), residues: 780 helix: 2.61 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 190 TYR 0.010 0.001 TYR A 116 PHE 0.016 0.001 PHE B 26 TRP 0.021 0.001 TRP B 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 6686) covalent geometry : angle 0.43896 / 0.23 ( 9100) hydrogen bonds : bond 0.04067 / 2.73 ( 537) hydrogen bonds : angle 3.71922 / 2.84 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.74 seconds wall clock time: 27 minutes 45.44 seconds (1665.44 seconds total)