Starting phenix.real_space_refine on Sat Aug 23 10:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.map" model { file = "/net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8skr_40565/08_2025/8skr_40565.cif" } resolution = 2.99 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6290 atoms to isotropic. 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 36 5.16 5 C 4024 2.51 5 N 1108 2.21 5 O 1162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6332 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3150 Classifications: {'peptide': 402} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3150 Classifications: {'peptide': 402} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.25 Number of scatterers: 6332 At special positions: 0 Unit cell: (106.425, 78.375, 65.175, 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 36 16.00 P 2 15.00 O 1162 8.00 N 1108 7.00 C 4024 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: 0.53 Conformation dependent library (CDL) restraints added in 376.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 56.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 118 through 124 Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 222 through 237 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 297 through 316 Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 333 through 366 removed outlier: 3.519A pdb=" N GLY A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.947A pdb=" N THR A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 77 through 91 Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 118 through 124 Processing helix chain 'C' and resid 133 through 149 Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 222 through 237 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 297 through 316 Proline residue: C 314 - end of helix Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 333 through 366 removed outlier: 3.519A pdb=" N GLY C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 removed outlier: 3.948A pdb=" N THR C 375 " --> pdb=" O TRP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 417 through 429 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.651A pdb=" N MET A 60 " --> pdb=" O TYR A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.761A pdb=" N GLY A 289 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL A 271 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP A 154 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 208 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 156 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 155 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A 179 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 157 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 383 Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.652A pdb=" N MET C 60 " --> pdb=" O TYR C 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 132 removed outlier: 3.761A pdb=" N GLY C 289 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C 271 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP C 154 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 208 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 156 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 155 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR C 179 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 157 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'C' and resid 381 through 383 340 hydrogen bonds defined for protein. 1014 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: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2055 1.34 - 1.46: 865 1.46 - 1.57: 3498 1.57 - 1.69: 2 1.69 - 1.81: 58 Bond restraints: 6478 Sorted by residual: bond pdb=" C2 PLP C 501 " pdb=" C3 PLP C 501 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C2 PLP A 501 " pdb=" C3 PLP A 501 " ideal model delta sigma weight residual 1.390 1.482 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 PLP A 501 " pdb=" C5 PLP A 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C4 PLP C 501 " pdb=" C5 PLP C 501 " ideal model delta sigma weight residual 1.390 1.478 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C3 PLP A 501 " pdb=" C4 PLP A 501 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 8411 1.24 - 2.48: 258 2.48 - 3.72: 60 3.72 - 4.95: 14 4.95 - 6.19: 13 Bond angle restraints: 8756 Sorted by residual: angle pdb=" C CYS C 212 " pdb=" CA CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.46e+00 4.69e-01 1.77e+01 angle pdb=" C CYS A 212 " pdb=" CA CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.46e+00 4.69e-01 1.77e+01 angle pdb=" C ASN C 318 " pdb=" N PRO C 319 " pdb=" CA PRO C 319 " ideal model delta sigma weight residual 120.38 116.59 3.79 1.03e+00 9.43e-01 1.35e+01 angle pdb=" CA ASN A 215 " pdb=" C ASN A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 121.01 117.66 3.35 9.50e-01 1.11e+00 1.25e+01 angle pdb=" CA THR A 166 " pdb=" C THR A 166 " pdb=" N PRO A 167 " ideal model delta sigma weight residual 120.52 117.60 2.92 8.30e-01 1.45e+00 1.24e+01 ... (remaining 8751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.49: 3811 28.49 - 56.97: 51 56.97 - 85.46: 2 85.46 - 113.94: 0 113.94 - 142.43: 2 Dihedral angle restraints: 3866 sinusoidal: 1568 harmonic: 2298 Sorted by residual: dihedral pdb=" C5 PLP A 501 " pdb=" C4 PLP A 501 " pdb=" C4A PLP A 501 " pdb=" O4A PLP A 501 " ideal model delta sinusoidal sigma weight residual 0.00 142.43 -142.43 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" C5 PLP C 501 " pdb=" C4 PLP C 501 " pdb=" C4A PLP C 501 " pdb=" O4A PLP C 501 " ideal model delta sinusoidal sigma weight residual 0.00 133.74 -133.74 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA CYS A 382 " pdb=" C CYS A 382 " pdb=" N PHE A 383 " pdb=" CA PHE A 383 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 571 0.026 - 0.051: 211 0.051 - 0.077: 94 0.077 - 0.103: 42 0.103 - 0.128: 18 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE A 201 " pdb=" N ILE A 201 " pdb=" C ILE A 201 " pdb=" CB ILE A 201 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE C 378 " pdb=" N ILE C 378 " pdb=" C ILE C 378 " pdb=" CB ILE C 378 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 933 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 383 " -0.012 2.00e-02 2.50e+03 1.19e-02 2.46e+00 pdb=" CG PHE C 383 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 383 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 383 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 383 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 383 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 383 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 383 " -0.012 2.00e-02 2.50e+03 1.19e-02 2.46e+00 pdb=" CG PHE A 383 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 383 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 383 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 383 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 383 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 383 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 215 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 216 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 904 2.75 - 3.29: 6408 3.29 - 3.83: 11196 3.83 - 4.36: 12658 4.36 - 4.90: 22579 Nonbonded interactions: 53745 Sorted by model distance: nonbonded pdb=" O PHE A 149 " pdb=" NH2 ARG A 153 " model vdw 2.219 3.120 nonbonded pdb=" O PHE C 149 " pdb=" NH2 ARG C 153 " model vdw 2.219 3.120 nonbonded pdb=" NH1 ARG A 355 " pdb=" O GLY A 379 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG C 355 " pdb=" O GLY C 379 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG A 81 " pdb=" OD1 ASN C 91 " model vdw 2.370 3.120 ... (remaining 53740 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.050 Find NCS groups from input model: 0.030 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.004 0.093 6478 Z= 0.216 Angle : 0.572 6.192 8756 Z= 0.339 Chirality : 0.037 0.128 936 Planarity : 0.004 0.037 1132 Dihedral : 10.590 142.428 2394 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 aren not related in a simple way. whole: 2.30 (0.29), residues: 800 helix: 2.82 (0.24), residues: 430 sheet: 0.08 (0.57), residues: 92 loop : -0.04 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 222 TYR 0.008 0.001 TYR C 284 PHE 0.028 0.001 PHE C 383 TRP 0.007 0.001 TRP A 162 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6478) covalent geometry : angle 0.57249 ( 8756) hydrogen bonds : bond 0.13675 ( 340) hydrogen bonds : angle 5.66948 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.8494 (m-80) cc_final: 0.8178 (m-80) REVERT: A 277 TYR cc_start: 0.8558 (m-80) cc_final: 0.8347 (m-80) REVERT: A 315 MET cc_start: 0.8540 (mtp) cc_final: 0.8334 (mtm) REVERT: A 378 ILE cc_start: 0.8462 (mm) cc_final: 0.8212 (tt) REVERT: C 277 TYR cc_start: 0.8549 (m-80) cc_final: 0.8348 (m-80) REVERT: C 315 MET cc_start: 0.8534 (mtp) cc_final: 0.8328 (mtm) REVERT: C 378 ILE cc_start: 0.8488 (mm) cc_final: 0.8265 (tt) outliers start: 0 outliers final: 2 residues processed: 67 average time/residue: 0.4633 time to fit residues: 32.9720 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain C residue 280 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068489 restraints weight = 13223.671| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.14 r_work: 0.2789 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6478 Z= 0.117 Angle : 0.449 4.932 8756 Z= 0.233 Chirality : 0.040 0.136 936 Planarity : 0.004 0.031 1132 Dihedral : 5.254 61.532 880 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % 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 aren not related in a simple way. whole: 2.59 (0.30), residues: 800 helix: 3.20 (0.25), residues: 432 sheet: 0.16 (0.54), residues: 90 loop : -0.17 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.012 0.001 TYR A 96 PHE 0.023 0.001 PHE A 383 TRP 0.008 0.001 TRP C 162 HIS 0.003 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6478) covalent geometry : angle 0.44907 ( 8756) hydrogen bonds : bond 0.03358 ( 340) hydrogen bonds : angle 4.41299 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.268 Fit side-chains REVERT: A 196 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 378 ILE cc_start: 0.8428 (mm) cc_final: 0.8218 (tt) REVERT: C 277 TYR cc_start: 0.8644 (m-80) cc_final: 0.8398 (m-80) REVERT: C 315 MET cc_start: 0.8760 (mtp) cc_final: 0.8553 (mtm) REVERT: C 378 ILE cc_start: 0.8447 (mm) cc_final: 0.8170 (tt) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.5060 time to fit residues: 26.3091 Evaluate side-chains 45 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.067171 restraints weight = 13352.321| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.18 r_work: 0.2762 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6478 Z= 0.118 Angle : 0.444 4.956 8756 Z= 0.228 Chirality : 0.040 0.125 936 Planarity : 0.004 0.031 1132 Dihedral : 5.102 64.519 876 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.45 % Allowed : 6.31 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.30), residues: 800 helix: 3.23 (0.25), residues: 432 sheet: 0.02 (0.53), residues: 90 loop : -0.20 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.014 0.001 TYR C 96 PHE 0.017 0.001 PHE A 383 TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6478) covalent geometry : angle 0.44409 ( 8756) hydrogen bonds : bond 0.03205 ( 340) hydrogen bonds : angle 4.21831 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.262 Fit side-chains REVERT: A 196 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 378 ILE cc_start: 0.8420 (mm) cc_final: 0.8219 (tt) REVERT: C 96 TYR cc_start: 0.8770 (m-80) cc_final: 0.8419 (m-80) REVERT: C 196 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: C 277 TYR cc_start: 0.8741 (m-80) cc_final: 0.8508 (m-80) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 0.4532 time to fit residues: 21.8248 Evaluate side-chains 42 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain C residue 196 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.066809 restraints weight = 13380.072| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.17 r_work: 0.2754 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6478 Z= 0.109 Angle : 0.438 5.342 8756 Z= 0.222 Chirality : 0.040 0.127 936 Planarity : 0.004 0.032 1132 Dihedral : 5.032 61.882 876 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.35 % Allowed : 7.21 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.30), residues: 800 helix: 3.24 (0.24), residues: 432 sheet: 0.10 (0.54), residues: 90 loop : -0.19 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.011 0.001 TYR A 96 PHE 0.014 0.001 PHE A 249 TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6478) covalent geometry : angle 0.43762 ( 8756) hydrogen bonds : bond 0.03044 ( 340) hydrogen bonds : angle 4.12435 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: C 96 TYR cc_start: 0.8848 (m-80) cc_final: 0.8522 (m-80) REVERT: C 196 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7689 (mp0) outliers start: 9 outliers final: 2 residues processed: 46 average time/residue: 0.4944 time to fit residues: 24.1981 Evaluate side-chains 43 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 392 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.063776 restraints weight = 13724.391| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.18 r_work: 0.2680 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6478 Z= 0.163 Angle : 0.463 5.348 8756 Z= 0.239 Chirality : 0.040 0.126 936 Planarity : 0.004 0.033 1132 Dihedral : 5.112 57.496 876 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 6.91 % Favored : 91.29 % 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 aren not related in a simple way. whole: 2.52 (0.30), residues: 800 helix: 3.18 (0.25), residues: 432 sheet: 0.04 (0.54), residues: 90 loop : -0.26 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.012 0.001 TYR A 96 PHE 0.015 0.001 PHE A 249 TRP 0.006 0.001 TRP A 162 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6478) covalent geometry : angle 0.46281 ( 8756) hydrogen bonds : bond 0.03411 ( 340) hydrogen bonds : angle 4.18009 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.168 Fit side-chains REVERT: A 196 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 244 MET cc_start: 0.9155 (ptm) cc_final: 0.8911 (ptm) REVERT: C 96 TYR cc_start: 0.8891 (m-80) cc_final: 0.8540 (m-80) REVERT: C 196 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: C 246 TYR cc_start: 0.8810 (m-10) cc_final: 0.8538 (m-10) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 0.3939 time to fit residues: 19.8449 Evaluate side-chains 47 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.064922 restraints weight = 13513.660| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.17 r_work: 0.2717 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6478 Z= 0.112 Angle : 0.448 6.806 8756 Z= 0.226 Chirality : 0.039 0.128 936 Planarity : 0.004 0.033 1132 Dihedral : 5.010 55.462 876 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.95 % Allowed : 7.81 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.30), residues: 800 helix: 3.23 (0.24), residues: 432 sheet: 0.01 (0.54), residues: 90 loop : -0.27 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.011 0.001 TYR A 96 PHE 0.016 0.001 PHE A 249 TRP 0.004 0.001 TRP A 162 HIS 0.001 0.000 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6478) covalent geometry : angle 0.44831 ( 8756) hydrogen bonds : bond 0.03046 ( 340) hydrogen bonds : angle 4.07552 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.158 Fit side-chains REVERT: A 196 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: C 96 TYR cc_start: 0.8822 (m-80) cc_final: 0.8497 (m-80) REVERT: C 196 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (mp0) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 0.4122 time to fit residues: 20.5577 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.061888 restraints weight = 13666.170| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.17 r_work: 0.2653 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6478 Z= 0.214 Angle : 0.503 5.636 8756 Z= 0.257 Chirality : 0.041 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 5.160 53.640 876 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.10 % Allowed : 8.56 % Favored : 89.34 % 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 aren not related in a simple way. whole: 2.46 (0.30), residues: 800 helix: 3.16 (0.25), residues: 432 sheet: 0.21 (0.54), residues: 86 loop : -0.41 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.013 0.002 TYR A 96 PHE 0.019 0.001 PHE C 249 TRP 0.005 0.001 TRP A 371 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 6478) covalent geometry : angle 0.50290 ( 8756) hydrogen bonds : bond 0.03650 ( 340) hydrogen bonds : angle 4.21767 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.191 Fit side-chains REVERT: A 196 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: C 96 TYR cc_start: 0.8823 (m-80) cc_final: 0.8568 (m-80) REVERT: C 196 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7808 (mp0) outliers start: 14 outliers final: 10 residues processed: 46 average time/residue: 0.4360 time to fit residues: 21.4898 Evaluate side-chains 47 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 293 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.064114 restraints weight = 13675.392| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.11 r_work: 0.2677 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6478 Z= 0.161 Angle : 0.478 7.385 8756 Z= 0.242 Chirality : 0.040 0.127 936 Planarity : 0.004 0.034 1132 Dihedral : 5.071 52.674 876 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.80 % Allowed : 9.01 % Favored : 89.19 % 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 aren not related in a simple way. whole: 2.48 (0.30), residues: 800 helix: 3.15 (0.25), residues: 432 sheet: 0.24 (0.54), residues: 86 loop : -0.36 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 325 TYR 0.012 0.001 TYR A 96 PHE 0.021 0.001 PHE C 249 TRP 0.005 0.001 TRP A 162 HIS 0.002 0.001 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6478) covalent geometry : angle 0.47770 ( 8756) hydrogen bonds : bond 0.03383 ( 340) hydrogen bonds : angle 4.16513 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.261 Fit side-chains REVERT: A 196 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: C 196 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (mp0) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.4080 time to fit residues: 18.9188 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064842 restraints weight = 13573.608| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.17 r_work: 0.2711 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6478 Z= 0.108 Angle : 0.458 6.267 8756 Z= 0.231 Chirality : 0.040 0.130 936 Planarity : 0.004 0.034 1132 Dihedral : 4.951 51.581 876 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 9.31 % Favored : 88.89 % 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 aren not related in a simple way. whole: 2.54 (0.30), residues: 800 helix: 3.21 (0.25), residues: 432 sheet: 0.27 (0.55), residues: 86 loop : -0.34 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 407 TYR 0.010 0.001 TYR C 96 PHE 0.026 0.001 PHE C 249 TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6478) covalent geometry : angle 0.45753 ( 8756) hydrogen bonds : bond 0.03044 ( 340) hydrogen bonds : angle 4.09169 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.273 Fit side-chains REVERT: A 196 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: C 196 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7802 (mp0) outliers start: 12 outliers final: 10 residues processed: 48 average time/residue: 0.4351 time to fit residues: 22.4815 Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 318 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.065149 restraints weight = 13394.978| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.16 r_work: 0.2718 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6478 Z= 0.117 Angle : 0.462 6.465 8756 Z= 0.235 Chirality : 0.040 0.130 936 Planarity : 0.004 0.034 1132 Dihedral : 4.945 49.675 876 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 9.91 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.30), residues: 800 helix: 3.18 (0.25), residues: 432 sheet: 0.24 (0.54), residues: 86 loop : -0.35 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.011 0.001 TYR A 401 PHE 0.033 0.001 PHE C 249 TRP 0.005 0.001 TRP C 162 HIS 0.001 0.000 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6478) covalent geometry : angle 0.46188 ( 8756) hydrogen bonds : bond 0.03059 ( 340) hydrogen bonds : angle 4.09409 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.161 Fit side-chains REVERT: A 196 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: C 196 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7808 (mp0) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.4459 time to fit residues: 20.4180 Evaluate side-chains 47 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 293 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.065243 restraints weight = 13609.217| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.16 r_work: 0.2722 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6478 Z= 0.108 Angle : 0.472 7.364 8756 Z= 0.236 Chirality : 0.040 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.919 47.773 876 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.50 % Allowed : 9.76 % Favored : 88.74 % 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 aren not related in a simple way. whole: 2.52 (0.31), residues: 800 helix: 3.23 (0.25), residues: 432 sheet: 0.27 (0.55), residues: 86 loop : -0.41 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.010 0.001 TYR A 401 PHE 0.032 0.001 PHE C 249 TRP 0.005 0.001 TRP C 162 HIS 0.001 0.000 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6478) covalent geometry : angle 0.47183 ( 8756) hydrogen bonds : bond 0.02960 ( 340) hydrogen bonds : angle 4.04785 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.35 seconds wall clock time: 22 minutes 29.25 seconds (1349.25 seconds total)