Starting phenix.real_space_refine on Tue Jun 10 07:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8skr_40565/06_2025/8skr_40565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8skr_40565/06_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_40565/06_2025/8skr_40565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8skr_40565/06_2025/8skr_40565.map" model { file = "/net/cci-nas-00/data/ceres_data/8skr_40565/06_2025/8skr_40565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8skr_40565/06_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-5710/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: 4.66, per 1000 atoms: 0.74 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.74 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: 2.98 Time building geometry restraints manager: 2.06 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: 0.04 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.850 Find NCS groups from input model: 0.140 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:16.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- 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 : 0.753 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: 1.3474 time to fit residues: 96.2511 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 : 0.830 ------------------------------------------------------------------------------- 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 = 0.076159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064487 restraints weight = 13396.906| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.16 r_work: 0.2698 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- 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 : 1.227 Fit side-chains REVERT: A 196 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 315 MET cc_start: 0.8773 (mtp) cc_final: 0.8561 (mtm) REVERT: A 378 ILE cc_start: 0.8427 (mm) cc_final: 0.8215 (tt) REVERT: C 378 ILE cc_start: 0.8492 (mm) cc_final: 0.8196 (tt) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.6061 time to fit residues: 80.4870 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 : 0.725 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 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: 0.8440 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.077478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.065696 restraints weight = 13447.851| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.18 r_work: 0.2721 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1596 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= 0.125 Angle : 0.447 4.926 8756 Z= 0.230 Chirality : 0.040 0.127 936 Planarity : 0.004 0.033 1132 Dihedral : 5.194 64.520 876 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.68 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: 2.59 (0.30), residues: 800 helix: 3.19 (0.25), residues: 432 sheet: 0.28 (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 0.016 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 0.03345 ( 340) hydrogen bonds : angle 4.23421 ( 1014) covalent geometry : bond 0.00294 ( 6478) covalent geometry : angle 0.44706 ( 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 : 1.568 Fit side-chains REVERT: A 60 MET cc_start: 0.8519 (mtm) cc_final: 0.7791 (mtp) REVERT: A 196 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 378 ILE cc_start: 0.8451 (mm) cc_final: 0.8243 (tt) REVERT: C 96 TYR cc_start: 0.8560 (m-80) cc_final: 0.8182 (m-80) REVERT: C 196 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: C 378 ILE cc_start: 0.8425 (mm) cc_final: 0.8203 (tt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 1.3648 time to fit residues: 67.6388 Evaluate side-chains 45 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.076579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.064824 restraints weight = 13728.811| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.18 r_work: 0.2700 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1823 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= 0.139 Angle : 0.447 5.107 8756 Z= 0.229 Chirality : 0.040 0.127 936 Planarity : 0.004 0.034 1132 Dihedral : 5.147 62.357 876 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.20 % Allowed : 6.76 % 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: 2.59 (0.30), residues: 800 helix: 3.20 (0.25), residues: 432 sheet: 0.25 (0.54), residues: 86 loop : -0.21 (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 0.013 0.001 PHE C 249 TYR 0.010 0.001 TYR C 96 ARG 0.002 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 340) hydrogen bonds : angle 4.15154 ( 1014) covalent geometry : bond 0.00329 ( 6478) covalent geometry : angle 0.44676 ( 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 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8573 (mtm) cc_final: 0.7814 (mtp) REVERT: A 196 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 378 ILE cc_start: 0.8449 (mm) cc_final: 0.8222 (tt) REVERT: C 96 TYR cc_start: 0.8602 (m-80) cc_final: 0.8283 (m-80) REVERT: C 196 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: C 378 ILE cc_start: 0.8406 (mm) cc_final: 0.8175 (tt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 1.2530 time to fit residues: 62.9346 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 : 0.725 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3079 r_free = 0.3079 target = 0.076246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.064499 restraints weight = 13635.115| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.16 r_work: 0.2696 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1959 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= 0.134 Angle : 0.442 5.149 8756 Z= 0.228 Chirality : 0.040 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 5.087 59.261 876 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.35 % Allowed : 7.81 % Favored : 90.84 % 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: 2.57 (0.30), residues: 800 helix: 3.19 (0.24), 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 33 HIS 0.002 0.000 HIS A 263 PHE 0.014 0.001 PHE C 249 TYR 0.009 0.001 TYR C 96 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 340) hydrogen bonds : angle 4.12375 ( 1014) covalent geometry : bond 0.00315 ( 6478) covalent geometry : angle 0.44207 ( 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 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8553 (mtm) cc_final: 0.7745 (mtp) REVERT: A 196 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 378 ILE cc_start: 0.8465 (mm) cc_final: 0.8234 (tt) REVERT: C 196 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 378 ILE cc_start: 0.8450 (mm) cc_final: 0.8225 (tt) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 1.6611 time to fit residues: 82.8734 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 392 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.076929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.065709 restraints weight = 13201.946| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.99 r_work: 0.2727 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6478 Z= 0.105 Angle : 0.424 5.023 8756 Z= 0.218 Chirality : 0.039 0.129 936 Planarity : 0.004 0.033 1132 Dihedral : 4.961 55.313 876 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.05 % Allowed : 8.26 % Favored : 90.69 % 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: 3.23 (0.24), residues: 432 sheet: -0.05 (0.54), residues: 90 loop : -0.18 (0.36), residues: 278 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 0.015 0.001 PHE C 249 TYR 0.010 0.001 TYR A 401 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 340) hydrogen bonds : angle 4.05064 ( 1014) covalent geometry : bond 0.00241 ( 6478) covalent geometry : angle 0.42438 ( 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 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 1.002 Fit side-chains REVERT: A 60 MET cc_start: 0.8566 (mtm) cc_final: 0.7749 (mtp) REVERT: A 196 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 244 MET cc_start: 0.9070 (ptm) cc_final: 0.8832 (ptm) REVERT: A 378 ILE cc_start: 0.8481 (mm) cc_final: 0.8274 (tt) REVERT: C 196 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7757 (mp0) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.0282 time to fit residues: 49.9260 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 : 0.706 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain C residue 292 THR 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: 1.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.076066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.064173 restraints weight = 13375.261| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.13 r_work: 0.2691 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2117 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= 0.138 Angle : 0.445 5.231 8756 Z= 0.228 Chirality : 0.040 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 4.979 52.864 876 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.80 % Allowed : 8.41 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.21 (0.25), residues: 432 sheet: -0.04 (0.54), residues: 90 loop : -0.22 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 33 HIS 0.002 0.001 HIS A 263 PHE 0.018 0.001 PHE C 249 TYR 0.008 0.001 TYR A 401 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 340) hydrogen bonds : angle 4.07299 ( 1014) covalent geometry : bond 0.00326 ( 6478) covalent geometry : angle 0.44524 ( 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: 12 poor density : 42 time to evaluate : 0.729 Fit side-chains REVERT: A 60 MET cc_start: 0.8545 (mtm) cc_final: 0.8338 (mtp) REVERT: A 196 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: C 196 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7817 (mp0) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.9755 time to fit residues: 48.3533 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 : 0.771 ------------------------------------------------------------------------------- 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 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 318 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.075845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.063951 restraints weight = 13338.072| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.15 r_work: 0.2693 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2193 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= 0.137 Angle : 0.449 5.311 8756 Z= 0.229 Chirality : 0.040 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 4.939 51.903 876 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 8.71 % Favored : 89.64 % 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: 2.67 (0.30), residues: 800 helix: 3.34 (0.25), residues: 420 sheet: 0.28 (0.55), residues: 86 loop : -0.15 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 33 HIS 0.002 0.001 HIS A 263 PHE 0.022 0.001 PHE C 249 TYR 0.007 0.001 TYR A 401 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 340) hydrogen bonds : angle 4.07581 ( 1014) covalent geometry : bond 0.00322 ( 6478) covalent geometry : angle 0.44859 ( 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 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.808 Fit side-chains REVERT: A 60 MET cc_start: 0.8548 (mtm) cc_final: 0.8332 (mtp) REVERT: A 196 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 383 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: C 196 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7816 (mp0) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 1.2490 time to fit residues: 62.0752 Evaluate side-chains 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.076432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.064582 restraints weight = 13455.505| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.15 r_work: 0.2694 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2211 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= 0.130 Angle : 0.455 6.084 8756 Z= 0.231 Chirality : 0.040 0.129 936 Planarity : 0.004 0.034 1132 Dihedral : 4.929 50.890 876 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 2.56 (0.30), residues: 800 helix: 3.22 (0.25), residues: 432 sheet: 0.23 (0.54), residues: 86 loop : -0.30 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 33 HIS 0.002 0.000 HIS A 263 PHE 0.027 0.001 PHE A 249 TYR 0.010 0.001 TYR C 401 ARG 0.001 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 340) hydrogen bonds : angle 4.06526 ( 1014) covalent geometry : bond 0.00305 ( 6478) covalent geometry : angle 0.45469 ( 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 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 1.515 Fit side-chains REVERT: A 60 MET cc_start: 0.8513 (mtm) cc_final: 0.8288 (mtp) REVERT: A 196 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 383 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: C 196 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7808 (mp0) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 1.0429 time to fit residues: 52.4477 Evaluate side-chains 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.075212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.063190 restraints weight = 13649.137| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.18 r_work: 0.2670 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.004 0.027 6478 Z= 0.169 Angle : 0.486 6.811 8756 Z= 0.248 Chirality : 0.040 0.127 936 Planarity : 0.004 0.034 1132 Dihedral : 5.049 50.192 876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 2.49 (0.30), residues: 800 helix: 3.19 (0.25), residues: 432 sheet: 0.13 (0.54), residues: 86 loop : -0.36 (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 A 263 PHE 0.030 0.001 PHE C 249 TYR 0.011 0.001 TYR A 401 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 340) hydrogen bonds : angle 4.12805 ( 1014) covalent geometry : bond 0.00400 ( 6478) covalent geometry : angle 0.48565 ( 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 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.674 Fit side-chains REVERT: A 60 MET cc_start: 0.8525 (mtm) cc_final: 0.8282 (mtp) REVERT: A 196 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 196 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7809 (mp0) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.9838 time to fit residues: 47.6894 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 : 0.762 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 43 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 = 0.3094 r_free = 0.3094 target = 0.077072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.066053 restraints weight = 13659.615| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.97 r_work: 0.2718 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2295 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= 0.119 Angle : 0.467 7.255 8756 Z= 0.236 Chirality : 0.040 0.129 936 Planarity : 0.004 0.034 1132 Dihedral : 4.932 48.537 876 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.50 % Allowed : 9.76 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.30), residues: 800 helix: 3.20 (0.24), residues: 432 sheet: 0.11 (0.54), residues: 86 loop : -0.36 (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 263 PHE 0.034 0.001 PHE C 249 TYR 0.011 0.001 TYR A 401 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 340) hydrogen bonds : angle 4.06418 ( 1014) covalent geometry : bond 0.00279 ( 6478) covalent geometry : angle 0.46659 ( 8756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3921.43 seconds wall clock time: 70 minutes 53.06 seconds (4253.06 seconds total)