Starting phenix.real_space_refine on Sat Nov 16 16:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_40565.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_40565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_40565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_40565.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skr_40565/11_2024/8skr_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.67, 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: 1.87 Conformation dependent library (CDL) restraints added in 977.6 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: 0.71 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: 2.13 Time building geometry restraints manager: 1.95 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.950 Find NCS groups from input model: 0.170 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.020 Total: 36.390 ------------------------------------------------------------------------------- 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= 0.234 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 *********************** 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 : 0.778 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: 0.9759 time to fit residues: 69.8887 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 : 0.918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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= 0.310 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 *********************** 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 : 0.905 Fit side-chains REVERT: A 196 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 315 MET cc_start: 0.8716 (mtp) cc_final: 0.8479 (mtm) REVERT: C 315 MET cc_start: 0.8721 (mtp) cc_final: 0.8519 (mtm) REVERT: C 378 ILE cc_start: 0.8603 (mm) cc_final: 0.8369 (tt) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.1962 time to fit residues: 59.9451 Evaluate side-chains 39 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6478 Z= 0.155 Angle : 0.436 4.797 8756 Z= 0.224 Chirality : 0.040 0.128 936 Planarity : 0.004 0.032 1132 Dihedral : 5.149 64.780 876 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: 2.61 (0.30), residues: 800 helix: 3.20 (0.24), residues: 432 sheet: 0.31 (0.54), residues: 86 loop : -0.21 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS C 263 PHE 0.015 0.001 PHE A 383 TYR 0.011 0.001 TYR C 96 ARG 0.001 0.000 ARG A 81 *********************** 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 : 0.701 Fit side-chains REVERT: A 60 MET cc_start: 0.8467 (mtm) cc_final: 0.7779 (mtp) REVERT: A 196 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 315 MET cc_start: 0.8706 (mtp) cc_final: 0.8463 (mtm) REVERT: C 96 TYR cc_start: 0.8547 (m-80) cc_final: 0.8155 (m-80) REVERT: C 196 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7347 (mp0) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 1.2804 time to fit residues: 63.3654 Evaluate side-chains 45 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1746 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= 0.190 Angle : 0.438 5.035 8756 Z= 0.225 Chirality : 0.040 0.127 936 Planarity : 0.004 0.033 1132 Dihedral : 5.097 62.824 876 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 6.61 % Favored : 91.89 % 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: 2.59 (0.30), residues: 800 helix: 3.20 (0.24), residues: 432 sheet: 0.27 (0.54), residues: 86 loop : -0.22 (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 0.014 0.001 PHE A 249 TYR 0.010 0.001 TYR C 96 ARG 0.001 0.000 ARG A 81 *********************** 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: 10 poor density : 41 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8547 (mtm) cc_final: 0.7810 (mtp) REVERT: A 196 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 315 MET cc_start: 0.8691 (mtp) cc_final: 0.8486 (mtm) REVERT: C 96 TYR cc_start: 0.8654 (m-80) cc_final: 0.8272 (m-80) REVERT: C 196 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7387 (mp0) outliers start: 10 outliers final: 2 residues processed: 45 average time/residue: 1.2522 time to fit residues: 59.9637 Evaluate side-chains 45 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 392 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6478 Z= 0.378 Angle : 0.507 5.657 8756 Z= 0.264 Chirality : 0.042 0.129 936 Planarity : 0.004 0.035 1132 Dihedral : 5.315 57.968 876 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.50 % Allowed : 7.66 % 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: 2.39 (0.30), residues: 800 helix: 3.08 (0.25), residues: 432 sheet: 0.16 (0.54), residues: 86 loop : -0.39 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 371 HIS 0.003 0.001 HIS A 263 PHE 0.014 0.001 PHE C 249 TYR 0.012 0.002 TYR C 96 ARG 0.003 0.001 ARG A 325 *********************** 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 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 315 MET cc_start: 0.8676 (mtp) cc_final: 0.8473 (mtm) REVERT: C 196 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 246 TYR cc_start: 0.8835 (m-10) cc_final: 0.8349 (m-80) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 1.5141 time to fit residues: 70.6493 Evaluate side-chains 43 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 318 ASN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 292 THR 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 69 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2137 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= 0.183 Angle : 0.441 5.304 8756 Z= 0.226 Chirality : 0.040 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 5.112 57.204 876 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.75 % Allowed : 9.31 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.25), residues: 432 sheet: 0.21 (0.54), residues: 86 loop : -0.35 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 33 HIS 0.002 0.000 HIS A 263 PHE 0.015 0.001 PHE C 249 TYR 0.009 0.001 TYR C 96 ARG 0.002 0.000 ARG A 325 *********************** 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 43 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.150 Fit side-chains REVERT: A 196 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 315 MET cc_start: 0.8678 (mtp) cc_final: 0.8458 (mtm) REVERT: C 96 TYR cc_start: 0.8692 (m-80) cc_final: 0.8453 (m-80) REVERT: C 196 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7485 (mp0) outliers start: 5 outliers final: 6 residues processed: 41 average time/residue: 1.1432 time to fit residues: 50.5116 Evaluate side-chains 42 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2186 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= 0.203 Angle : 0.449 5.368 8756 Z= 0.228 Chirality : 0.040 0.129 936 Planarity : 0.004 0.034 1132 Dihedral : 5.046 55.474 876 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 2.51 (0.30), residues: 800 helix: 3.18 (0.24), residues: 432 sheet: 0.24 (0.55), residues: 86 loop : -0.34 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.002 0.000 HIS A 263 PHE 0.020 0.001 PHE C 249 TYR 0.009 0.001 TYR C 96 ARG 0.002 0.000 ARG C 325 *********************** 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 51 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.846 Fit side-chains REVERT: A 60 MET cc_start: 0.8447 (mtm) cc_final: 0.7861 (mtp) REVERT: A 196 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: A 315 MET cc_start: 0.8668 (mtp) cc_final: 0.8443 (mtm) REVERT: C 196 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7488 (mp0) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 1.0763 time to fit residues: 51.1229 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 : 0.771 ------------------------------------------------------------------------------- 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 292 THR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 293 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2230 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= 0.214 Angle : 0.452 5.569 8756 Z= 0.230 Chirality : 0.040 0.129 936 Planarity : 0.004 0.034 1132 Dihedral : 5.005 52.831 876 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.65 % Allowed : 9.01 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.50 (0.30), residues: 800 helix: 3.18 (0.25), residues: 432 sheet: 0.17 (0.54), residues: 86 loop : -0.33 (0.36), residues: 282 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 0.022 0.001 PHE C 249 TYR 0.008 0.001 TYR A 401 ARG 0.002 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.690 Fit side-chains REVERT: A 60 MET cc_start: 0.8473 (mtm) cc_final: 0.7864 (mtp) REVERT: A 196 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 315 MET cc_start: 0.8667 (mtp) cc_final: 0.8450 (mtm) REVERT: A 383 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: C 196 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: C 383 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7784 (m-80) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.9759 time to fit residues: 47.3623 Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 383 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2244 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= 0.209 Angle : 0.458 6.349 8756 Z= 0.232 Chirality : 0.040 0.128 936 Planarity : 0.004 0.034 1132 Dihedral : 5.007 52.372 876 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.47 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: 2.52 (0.30), residues: 800 helix: 3.19 (0.25), residues: 432 sheet: 0.15 (0.54), residues: 86 loop : -0.32 (0.36), residues: 282 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 0.027 0.001 PHE A 249 TYR 0.009 0.001 TYR A 401 ARG 0.002 0.000 ARG C 325 *********************** 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 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.805 Fit side-chains REVERT: A 60 MET cc_start: 0.8476 (mtm) cc_final: 0.7879 (mtp) REVERT: A 196 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 315 MET cc_start: 0.8663 (mtp) cc_final: 0.8445 (mtm) REVERT: A 383 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 196 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: C 383 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7749 (m-80) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 1.0394 time to fit residues: 50.4442 Evaluate side-chains 50 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 383 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2237 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= 0.165 Angle : 0.453 6.881 8756 Z= 0.230 Chirality : 0.039 0.130 936 Planarity : 0.004 0.033 1132 Dihedral : 4.957 49.868 876 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 9.31 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.21 (0.24), residues: 432 sheet: 0.19 (0.54), residues: 86 loop : -0.33 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 162 HIS 0.001 0.000 HIS A 263 PHE 0.032 0.001 PHE C 249 TYR 0.011 0.001 TYR A 401 ARG 0.001 0.000 ARG C 81 ********************** 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 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.741 Fit side-chains REVERT: A 60 MET cc_start: 0.8421 (mtm) cc_final: 0.7799 (mtp) REVERT: A 196 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 315 MET cc_start: 0.8648 (mtp) cc_final: 0.8416 (mtm) REVERT: C 196 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7521 (mp0) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.9311 time to fit residues: 48.2846 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 : 0.756 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.076472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065024 restraints weight = 13371.331| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.06 r_work: 0.2710 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6478 Z= 0.187 Angle : 0.460 6.521 8756 Z= 0.234 Chirality : 0.039 0.132 936 Planarity : 0.004 0.033 1132 Dihedral : 4.973 48.287 876 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 9.76 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.21 (0.24), residues: 432 sheet: 0.15 (0.54), residues: 86 loop : -0.34 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.002 0.000 HIS C 263 PHE 0.039 0.001 PHE C 249 TYR 0.011 0.001 TYR A 401 ARG 0.001 0.000 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.48 seconds wall clock time: 35 minutes 2.29 seconds (2102.29 seconds total)