Starting phenix.real_space_refine on Wed May 14 05:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8skr_40565/05_2025/8skr_40565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8skr_40565/05_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_40565/05_2025/8skr_40565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8skr_40565/05_2025/8skr_40565.map" model { file = "/net/cci-nas-00/data/ceres_data/8skr_40565/05_2025/8skr_40565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8skr_40565/05_2025/8skr_40565.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.23, per 1000 atoms: 0.67 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: 1.55 Conformation dependent library (CDL) restraints added in 887.4 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: 0.69 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: 1.78 Time building geometry restraints manager: 1.81 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: 0.03 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.970 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 : 7.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 162 HIS 0.002 0.000 HIS A 214 PHE 0.028 0.001 PHE C 383 TYR 0.008 0.001 TYR C 284 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.13675 ( 340) hydrogen bonds : angle 5.66948 ( 1014) covalent geometry : bond 0.00377 ( 6478) covalent geometry : angle 0.57249 ( 8756) *********************** 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 : 0.689 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: 0.9499 time to fit residues: 68.0090 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 : 0.703 ------------------------------------------------------------------------------- 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 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.0000 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064483 restraints weight = 13397.122| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.17 r_work: 0.2699 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6478 Z= 0.199 Angle : 0.499 5.348 8756 Z= 0.260 Chirality : 0.042 0.127 936 Planarity : 0.004 0.031 1132 Dihedral : 5.442 63.781 880 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.75 % Allowed : 4.80 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.30), residues: 800 helix: 3.16 (0.25), residues: 432 sheet: 0.01 (0.54), residues: 90 loop : -0.20 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.004 0.001 HIS C 214 PHE 0.025 0.001 PHE A 383 TYR 0.015 0.002 TYR A 96 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 340) hydrogen bonds : angle 4.50396 ( 1014) covalent geometry : bond 0.00465 ( 6478) covalent geometry : angle 0.49929 ( 8756) *********************** 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: 5 poor density : 45 time to evaluate : 0.732 Fit side-chains REVERT: A 196 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 315 MET cc_start: 0.8774 (mtp) cc_final: 0.8563 (mtm) REVERT: A 378 ILE cc_start: 0.8432 (mm) cc_final: 0.8220 (tt) REVERT: C 378 ILE cc_start: 0.8496 (mm) cc_final: 0.8200 (tt) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.1167 time to fit residues: 55.8773 Evaluate side-chains 40 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 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 = 0.3109 r_free = 0.3109 target = 0.077844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.066054 restraints weight = 13415.381| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.16 r_work: 0.2731 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1581 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= 0.119 Angle : 0.443 4.871 8756 Z= 0.228 Chirality : 0.040 0.129 936 Planarity : 0.004 0.033 1132 Dihedral : 5.174 64.665 876 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.60 % Allowed : 6.76 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 800 helix: 3.19 (0.25), residues: 432 sheet: 0.29 (0.54), residues: 86 loop : -0.20 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.002 0.000 HIS C 263 PHE 0.015 0.001 PHE A 383 TYR 0.012 0.001 TYR C 96 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 340) hydrogen bonds : angle 4.21964 ( 1014) covalent geometry : bond 0.00279 ( 6478) covalent geometry : angle 0.44320 ( 8756) *********************** 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: 4 poor density : 44 time to evaluate : 0.699 Fit side-chains REVERT: A 60 MET cc_start: 0.8500 (mtm) cc_final: 0.7762 (mtp) REVERT: A 196 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 378 ILE cc_start: 0.8445 (mm) cc_final: 0.8243 (tt) REVERT: C 96 TYR cc_start: 0.8559 (m-80) cc_final: 0.8186 (m-80) REVERT: C 196 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: C 378 ILE cc_start: 0.8434 (mm) cc_final: 0.8218 (tt) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.9685 time to fit residues: 47.9926 Evaluate side-chains 44 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.076514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.064737 restraints weight = 13769.248| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.21 r_work: 0.2698 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6478 Z= 0.143 Angle : 0.453 5.096 8756 Z= 0.232 Chirality : 0.040 0.127 936 Planarity : 0.004 0.034 1132 Dihedral : 5.148 62.521 876 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 6.46 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.30), residues: 800 helix: 3.19 (0.25), residues: 432 sheet: 0.19 (0.54), residues: 86 loop : -0.20 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.002 0.000 HIS A 263 PHE 0.012 0.001 PHE C 249 TYR 0.011 0.001 TYR C 96 ARG 0.002 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 340) hydrogen bonds : angle 4.16979 ( 1014) covalent geometry : bond 0.00340 ( 6478) covalent geometry : angle 0.45332 ( 8756) *********************** 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 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8560 (mtm) cc_final: 0.7803 (mtp) REVERT: A 196 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 378 ILE cc_start: 0.8433 (mm) cc_final: 0.8201 (tt) REVERT: C 96 TYR cc_start: 0.8596 (m-80) cc_final: 0.8268 (m-80) REVERT: C 196 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 378 ILE cc_start: 0.8406 (mm) cc_final: 0.8174 (tt) outliers start: 10 outliers final: 5 residues processed: 46 average time/residue: 1.0970 time to fit residues: 53.9434 Evaluate side-chains 47 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 392 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 318 ASN 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 68 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 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 = 0.3105 r_free = 0.3105 target = 0.077478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.065800 restraints weight = 13483.683| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.15 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: 0.8229 moved from start: 0.1854 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= 0.112 Angle : 0.426 5.050 8756 Z= 0.219 Chirality : 0.040 0.129 936 Planarity : 0.004 0.033 1132 Dihedral : 5.034 59.916 876 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.60 % Allowed : 8.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.30), residues: 800 helix: 3.19 (0.24), residues: 432 sheet: 0.27 (0.54), residues: 86 loop : -0.20 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.002 0.000 HIS A 263 PHE 0.014 0.001 PHE C 249 TYR 0.010 0.001 TYR A 401 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 340) hydrogen bonds : angle 4.09498 ( 1014) covalent geometry : bond 0.00262 ( 6478) covalent geometry : angle 0.42648 ( 8756) *********************** 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 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.777 Fit side-chains REVERT: A 60 MET cc_start: 0.8534 (mtm) cc_final: 0.7742 (mtp) REVERT: A 196 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 378 ILE cc_start: 0.8466 (mm) cc_final: 0.8259 (tt) REVERT: C 96 TYR cc_start: 0.8588 (m-80) cc_final: 0.8307 (m-80) REVERT: C 196 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 246 TYR cc_start: 0.8754 (m-10) cc_final: 0.8454 (m-10) REVERT: C 378 ILE cc_start: 0.8434 (mm) cc_final: 0.8213 (tt) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 1.0738 time to fit residues: 53.9917 Evaluate side-chains 48 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.078854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067500 restraints weight = 13328.452| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.10 r_work: 0.2747 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6478 Z= 0.091 Angle : 0.421 4.954 8756 Z= 0.215 Chirality : 0.039 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.926 57.627 876 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.35 % Allowed : 8.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.30), residues: 800 helix: 3.24 (0.24), residues: 432 sheet: 0.01 (0.54), residues: 90 loop : -0.15 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.001 0.000 HIS A 263 PHE 0.015 0.001 PHE A 249 TYR 0.009 0.001 TYR A 401 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 340) hydrogen bonds : angle 4.01798 ( 1014) covalent geometry : bond 0.00206 ( 6478) covalent geometry : angle 0.42059 ( 8756) *********************** 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 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.707 Fit side-chains REVERT: A 60 MET cc_start: 0.8522 (mtm) cc_final: 0.7700 (mtp) REVERT: A 196 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: A 378 ILE cc_start: 0.8452 (mm) cc_final: 0.8245 (tt) REVERT: C 96 TYR cc_start: 0.8576 (m-80) cc_final: 0.8301 (m-80) REVERT: C 196 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7791 (mp0) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.9998 time to fit residues: 48.3698 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.077293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065386 restraints weight = 13358.832| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.18 r_work: 0.2718 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2019 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= 0.112 Angle : 0.431 5.100 8756 Z= 0.220 Chirality : 0.039 0.129 936 Planarity : 0.004 0.033 1132 Dihedral : 4.887 54.421 876 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 8.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 800 helix: 3.24 (0.24), residues: 432 sheet: 0.28 (0.54), residues: 86 loop : -0.28 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.001 0.000 HIS C 263 PHE 0.020 0.001 PHE C 249 TYR 0.008 0.001 TYR C 96 ARG 0.001 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 340) hydrogen bonds : angle 4.02007 ( 1014) covalent geometry : bond 0.00262 ( 6478) covalent geometry : angle 0.43052 ( 8756) *********************** 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 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.718 Fit side-chains REVERT: A 196 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 96 TYR cc_start: 0.8612 (m-80) cc_final: 0.8363 (m-80) REVERT: C 196 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7779 (mp0) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.9718 time to fit residues: 49.1459 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 : 0.676 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.076158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.064088 restraints weight = 13363.560| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.13 r_work: 0.2687 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6478 Z= 0.150 Angle : 0.459 5.300 8756 Z= 0.235 Chirality : 0.040 0.128 936 Planarity : 0.004 0.033 1132 Dihedral : 4.956 52.159 876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.80 % Allowed : 8.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 800 helix: 3.35 (0.25), residues: 420 sheet: 0.21 (0.54), residues: 86 loop : -0.19 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.002 0.001 HIS C 263 PHE 0.023 0.001 PHE C 249 TYR 0.010 0.001 TYR C 401 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 340) hydrogen bonds : angle 4.10199 ( 1014) covalent geometry : bond 0.00356 ( 6478) covalent geometry : angle 0.45850 ( 8756) *********************** 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 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.678 Fit side-chains REVERT: A 196 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: C 196 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7798 (mp0) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.9461 time to fit residues: 46.9272 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 : 0.696 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.076517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064522 restraints weight = 13429.628| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.16 r_work: 0.2706 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6478 Z= 0.124 Angle : 0.454 5.605 8756 Z= 0.232 Chirality : 0.039 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 4.918 50.424 876 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 9.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.30), residues: 800 helix: 3.21 (0.25), residues: 432 sheet: 0.15 (0.53), residues: 86 loop : -0.37 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 33 HIS 0.001 0.000 HIS A 263 PHE 0.028 0.001 PHE A 249 TYR 0.010 0.001 TYR C 401 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 340) hydrogen bonds : angle 4.06547 ( 1014) covalent geometry : bond 0.00290 ( 6478) covalent geometry : angle 0.45432 ( 8756) *********************** 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 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.783 Fit side-chains REVERT: A 196 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: C 196 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7813 (mp0) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.9863 time to fit residues: 47.9537 Evaluate side-chains 48 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3110 r_free = 0.3110 target = 0.077922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.066227 restraints weight = 13357.335| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.10 r_work: 0.2745 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6478 Z= 0.097 Angle : 0.445 6.253 8756 Z= 0.226 Chirality : 0.039 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.787 49.041 876 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 9.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.30), residues: 800 helix: 3.23 (0.24), residues: 432 sheet: 0.15 (0.53), residues: 86 loop : -0.33 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS C 214 PHE 0.032 0.001 PHE C 249 TYR 0.007 0.001 TYR C 401 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 340) hydrogen bonds : angle 4.00338 ( 1014) covalent geometry : bond 0.00222 ( 6478) covalent geometry : angle 0.44461 ( 8756) ********************** 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 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.685 Fit side-chains REVERT: A 196 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 196 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: C 383 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7416 (m-80) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.9459 time to fit residues: 46.8750 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 293 MET Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 383 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN C 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065394 restraints weight = 13636.127| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.05 r_work: 0.2722 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6478 Z= 0.122 Angle : 0.456 6.309 8756 Z= 0.232 Chirality : 0.039 0.129 936 Planarity : 0.004 0.034 1132 Dihedral : 4.825 46.897 876 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.10 % Allowed : 9.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.30), residues: 800 helix: 3.22 (0.25), residues: 432 sheet: 0.07 (0.53), residues: 86 loop : -0.30 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 162 HIS 0.002 0.001 HIS C 263 PHE 0.036 0.001 PHE A 249 TYR 0.007 0.001 TYR C 179 ARG 0.001 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 340) hydrogen bonds : angle 4.02840 ( 1014) covalent geometry : bond 0.00285 ( 6478) covalent geometry : angle 0.45649 ( 8756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.78 seconds wall clock time: 51 minutes 46.77 seconds (3106.77 seconds total)