Starting phenix.real_space_refine on Fri Jul 3 01:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8skr_40565/07_2026/8skr_40565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8skr_40565/07_2026/8skr_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_40565/07_2026/8skr_40565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8skr_40565/07_2026/8skr_40565.map" model { file = "/net/cci-nas-00/data/ceres_data/8skr_40565/07_2026/8skr_40565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8skr_40565/07_2026/8skr_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-dev-6108/lib/python3.11/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: 1.55, per 1000 atoms: 0.24 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: 0.43 Conformation dependent library (CDL) restraints added in 355.1 milliseconds 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: 0.16 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: 0.99 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: 1.22 - 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=" O4P PLP C 501 " pdb=" P PLP C 501 " ideal model delta sigma weight residual 1.687 1.607 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " ideal model delta sigma weight residual 1.687 1.609 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C3 PLP A 501 " pdb=" C4 PLP A 501 " ideal model delta sigma weight residual 1.402 1.477 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C3 PLP C 501 " pdb=" C4 PLP C 501 " ideal model delta sigma weight residual 1.402 1.477 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C4 PLP A 501 " pdb=" C5 PLP A 501 " ideal model delta sigma weight residual 1.410 1.481 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 8414 1.24 - 2.48: 265 2.48 - 3.72: 62 3.72 - 4.95: 7 4.95 - 6.19: 8 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 - 11.00: 3452 11.00 - 22.00: 306 22.00 - 33.00: 75 33.00 - 44.00: 35 44.00 - 55.00: 6 Dihedral angle restraints: 3874 sinusoidal: 1576 harmonic: 2298 Sorted by residual: 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 dihedral pdb=" CA CYS C 382 " pdb=" C CYS C 382 " pdb=" N PHE C 383 " pdb=" CA PHE C 383 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB LYS A 296 " pdb=" CG LYS A 296 " pdb=" CD LYS A 296 " pdb=" CE LYS A 296 " ideal model delta sinusoidal sigma weight residual -180.00 -125.00 -55.00 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 3871 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.060 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 0.080 6478 Z= 0.211 Angle : 0.547 6.192 8756 Z= 0.334 Chirality : 0.037 0.128 936 Planarity : 0.004 0.037 1132 Dihedral : 9.846 54.998 2402 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 are 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/Z covalent geometry : bond 0.00365 / 0.21 ( 6478) covalent geometry : angle 0.54676 / 0.33 ( 8756) hydrogen bonds : bond 0.13675 / 9.29 ( 340) hydrogen bonds : angle 5.66948 / 4.08 ( 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 : 0.239 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: 0.8539 (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: 0.4406 time to fit residues: 31.5042 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 : 0.176 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3154 r_free = 0.3154 target = 0.080158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.068374 restraints weight = 13252.186| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.18 r_work: 0.2788 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6478 Z= 0.120 Angle : 0.449 5.215 8756 Z= 0.235 Chirality : 0.040 0.136 936 Planarity : 0.004 0.030 1132 Dihedral : 4.888 34.834 888 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 are not related in a simple way. whole: 2.60 (0.30), residues: 800 helix: 3.20 (0.25), residues: 432 sheet: 0.17 (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 0.010 0.001 TRP C 162 HIS 0.003 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6478) covalent geometry : angle 0.44876 / 0.23 ( 8756) hydrogen bonds : bond 0.03361 / 2.21 ( 340) hydrogen bonds : angle 4.41770 / 3.16 ( 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 : 0.256 Fit side-chains REVERT: A 196 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 378 ILE cc_start: 0.8416 (mm) cc_final: 0.8198 (tt) REVERT: C 378 ILE cc_start: 0.8447 (mm) cc_final: 0.8172 (tt) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.5464 time to fit residues: 28.3728 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 : 0.237 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.078543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066981 restraints weight = 13310.019| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.11 r_work: 0.2754 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6478 Z= 0.121 Angle : 0.442 5.111 8756 Z= 0.229 Chirality : 0.040 0.125 936 Planarity : 0.004 0.032 1132 Dihedral : 4.741 32.111 884 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.30 % Allowed : 6.76 % Favored : 92.94 % 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: 2.57 (0.29), residues: 800 helix: 3.20 (0.24), residues: 432 sheet: 0.28 (0.53), residues: 86 loop : -0.27 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.013 0.001 TYR A 96 PHE 0.018 0.001 PHE A 383 TRP 0.008 0.001 TRP A 162 HIS 0.002 0.000 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6478) covalent geometry : angle 0.44174 / 0.23 ( 8756) hydrogen bonds : bond 0.03263 / 2.13 ( 340) hydrogen bonds : angle 4.18752 / 2.94 ( 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: 2 poor density : 46 time to evaluate : 0.267 Fit side-chains REVERT: A 196 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: C 96 TYR cc_start: 0.8836 (m-80) cc_final: 0.8405 (m-80) REVERT: C 196 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7783 (mp0) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.4871 time to fit residues: 23.8787 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 : 0.233 ------------------------------------------------------------------------------- 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: 0.0370 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.079103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.067342 restraints weight = 13303.392| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.20 r_work: 0.2765 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6478 Z= 0.104 Angle : 0.429 5.471 8756 Z= 0.219 Chirality : 0.040 0.128 936 Planarity : 0.004 0.032 1132 Dihedral : 4.648 31.801 884 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.05 % Allowed : 7.51 % 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 are not related in a simple way. whole: 2.57 (0.30), residues: 800 helix: 3.21 (0.24), residues: 432 sheet: 0.05 (0.54), residues: 90 loop : -0.21 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.011 0.001 TYR A 96 PHE 0.015 0.001 PHE C 249 TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 6478) covalent geometry : angle 0.42906 / 0.22 ( 8756) hydrogen bonds : bond 0.03001 / 1.96 ( 340) hydrogen bonds : angle 4.10288 / 2.87 ( 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 48 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: C 96 TYR cc_start: 0.8859 (m-80) cc_final: 0.8514 (m-80) REVERT: C 196 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 7 outliers final: 1 residues processed: 44 average time/residue: 0.5519 time to fit residues: 25.7521 Evaluate side-chains 41 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.074596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.062849 restraints weight = 13743.434| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.17 r_work: 0.2668 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6478 Z= 0.187 Angle : 0.478 5.587 8756 Z= 0.249 Chirality : 0.041 0.126 936 Planarity : 0.004 0.034 1132 Dihedral : 4.861 32.450 884 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.65 % Allowed : 7.36 % Favored : 90.99 % 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: 2.45 (0.30), residues: 800 helix: 3.16 (0.25), residues: 432 sheet: -0.02 (0.54), residues: 90 loop : -0.33 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 407 TYR 0.013 0.002 TYR A 96 PHE 0.018 0.001 PHE C 249 TRP 0.006 0.001 TRP A 162 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 6478) covalent geometry : angle 0.47812 / 0.25 ( 8756) hydrogen bonds : bond 0.03608 / 2.34 ( 340) hydrogen bonds : angle 4.21380 / 2.96 ( 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 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 244 MET cc_start: 0.9162 (ptm) cc_final: 0.8955 (ptm) REVERT: C 96 TYR cc_start: 0.8854 (m-80) cc_final: 0.8510 (m-80) REVERT: C 196 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7792 (mp0) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.4792 time to fit residues: 23.0621 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 A residue 318 ASN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 318 ASN 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: 1.9990 chunk 33 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.077442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065320 restraints weight = 13423.692| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.16 r_work: 0.2713 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2083 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= 0.106 Angle : 0.424 5.381 8756 Z= 0.219 Chirality : 0.039 0.128 936 Planarity : 0.004 0.033 1132 Dihedral : 4.802 31.128 884 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.50 % Allowed : 8.26 % 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 are not related in a simple way. whole: 2.54 (0.30), residues: 800 helix: 3.23 (0.24), residues: 432 sheet: -0.03 (0.54), residues: 90 loop : -0.28 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.009 0.001 TYR A 96 PHE 0.019 0.001 PHE C 249 TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6478) covalent geometry : angle 0.42444 / 0.22 ( 8756) hydrogen bonds : bond 0.03039 / 1.99 ( 340) hydrogen bonds : angle 4.07205 / 2.86 ( 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: 10 poor density : 45 time to evaluate : 0.183 Fit side-chains REVERT: A 196 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: C 96 TYR cc_start: 0.8770 (m-80) cc_final: 0.8480 (m-80) REVERT: C 196 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7742 (mp0) outliers start: 10 outliers final: 6 residues processed: 49 average time/residue: 0.4870 time to fit residues: 25.4617 Evaluate side-chains 46 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.075818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.063615 restraints weight = 13442.141| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.19 r_work: 0.2682 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6478 Z= 0.159 Angle : 0.470 7.327 8756 Z= 0.238 Chirality : 0.040 0.127 936 Planarity : 0.004 0.033 1132 Dihedral : 4.796 31.031 884 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.65 % Allowed : 9.01 % 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 are not related in a simple way. whole: 2.51 (0.30), residues: 800 helix: 3.21 (0.25), residues: 432 sheet: -0.04 (0.55), residues: 90 loop : -0.29 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 325 TYR 0.012 0.001 TYR A 96 PHE 0.020 0.001 PHE C 249 TRP 0.005 0.001 TRP A 162 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 6478) covalent geometry : angle 0.46985 / 0.24 ( 8756) hydrogen bonds : bond 0.03336 / 2.17 ( 340) hydrogen bonds : angle 4.11483 / 2.89 ( 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 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.252 Fit side-chains REVERT: A 196 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 96 TYR cc_start: 0.8773 (m-80) cc_final: 0.8520 (m-80) REVERT: C 196 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7797 (mp0) outliers start: 11 outliers final: 12 residues processed: 46 average time/residue: 0.4542 time to fit residues: 22.4504 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 A residue 318 ASN 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 318 ASN 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: 3.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.076919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.064669 restraints weight = 13447.587| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.19 r_work: 0.2704 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6478 Z= 0.123 Angle : 0.455 6.386 8756 Z= 0.230 Chirality : 0.040 0.128 936 Planarity : 0.004 0.033 1132 Dihedral : 4.784 29.890 884 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.50 % Allowed : 9.31 % 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 are not related in a simple way. whole: 2.56 (0.30), residues: 800 helix: 3.22 (0.25), residues: 432 sheet: 0.29 (0.55), residues: 86 loop : -0.33 (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 A 96 PHE 0.023 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/Z covalent geometry : bond 0.00289 / 0.12 ( 6478) covalent geometry : angle 0.45525 / 0.23 ( 8756) hydrogen bonds : bond 0.03139 / 2.05 ( 340) hydrogen bonds : angle 4.07850 / 2.86 ( 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 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.256 Fit side-chains REVERT: A 196 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: C 96 TYR cc_start: 0.8740 (m-80) cc_final: 0.8470 (m-80) REVERT: C 196 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7803 (mp0) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.3978 time to fit residues: 20.0608 Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 292 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 318 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.076096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.064052 restraints weight = 13611.693| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.18 r_work: 0.2685 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6478 Z= 0.147 Angle : 0.473 6.476 8756 Z= 0.240 Chirality : 0.040 0.128 936 Planarity : 0.004 0.033 1132 Dihedral : 4.817 29.801 884 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.65 % Allowed : 9.31 % Favored : 89.04 % 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: 2.54 (0.30), residues: 800 helix: 3.21 (0.25), residues: 432 sheet: 0.20 (0.54), residues: 86 loop : -0.32 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 407 TYR 0.012 0.001 TYR A 96 PHE 0.027 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/Z covalent geometry : bond 0.00347 / 0.15 ( 6478) covalent geometry : angle 0.47273 / 0.24 ( 8756) hydrogen bonds : bond 0.03260 / 2.13 ( 340) hydrogen bonds : angle 4.10441 / 2.88 ( 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 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.255 Fit side-chains REVERT: A 196 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 383 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: C 96 TYR cc_start: 0.8718 (m-80) cc_final: 0.8428 (m-80) REVERT: C 196 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (mp0) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.4129 time to fit residues: 21.1669 Evaluate side-chains 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 A residue 383 PHE 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 318 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.077483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065336 restraints weight = 13298.060| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.18 r_work: 0.2721 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2314 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= 0.111 Angle : 0.464 6.454 8756 Z= 0.236 Chirality : 0.039 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.798 29.068 884 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 9.76 % 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 are not related in a simple way. whole: 2.56 (0.30), residues: 800 helix: 3.23 (0.25), residues: 432 sheet: 0.25 (0.55), residues: 86 loop : -0.35 (0.36), 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 0.006 0.001 TRP C 162 HIS 0.001 0.000 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6478) covalent geometry : angle 0.46432 / 0.24 ( 8756) hydrogen bonds : bond 0.03023 / 1.98 ( 340) hydrogen bonds : angle 4.05834 / 2.85 ( 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 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.261 Fit side-chains REVERT: A 196 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 383 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: C 196 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7819 (mp0) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.4804 time to fit residues: 24.1809 Evaluate side-chains 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 A residue 383 PHE 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 318 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.078287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.066015 restraints weight = 13435.276| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.21 r_work: 0.2735 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2296 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= 0.102 Angle : 0.447 6.396 8756 Z= 0.229 Chirality : 0.039 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.723 28.025 884 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 10.06 % Favored : 88.59 % 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: 2.56 (0.31), residues: 800 helix: 3.24 (0.25), residues: 432 sheet: 0.23 (0.55), residues: 86 loop : -0.34 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.011 0.001 TYR C 401 PHE 0.032 0.001 PHE A 249 TRP 0.006 0.001 TRP C 162 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 6478) covalent geometry : angle 0.44666 / 0.23 ( 8756) hydrogen bonds : bond 0.02916 / 1.91 ( 340) hydrogen bonds : angle 4.02443 / 2.83 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.09 seconds wall clock time: 25 minutes 58.03 seconds (1558.03 seconds total)