Starting phenix.real_space_refine on Fri Dec 27 14:31:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.map" model { file = "/net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aur_15673/12_2024/8aur_15673.cif" } resolution = 3.47 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3390 2.51 5 N 894 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5409 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "B" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "C" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Time building chain proxies: 3.84, per 1000 atoms: 0.71 Number of scatterers: 5409 At special positions: 0 Unit cell: (64.428, 72.072, 220.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1113 8.00 N 894 7.00 C 3390 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: 1.24 Conformation dependent library (CDL) restraints added in 656.9 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 19.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS B 160 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS C 160 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 250 through 254 Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 60 removed outlier: 11.518A pdb=" N SER B 58 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N THR A 38 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N LEU B 60 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 40 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 82 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 168 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.121A pdb=" N SER A 58 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 40 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 31 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 82 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 168 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN A 195 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 114 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 197 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN B 195 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 114 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU B 197 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN C 195 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 114 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 197 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.541A pdb=" N VAL C 168 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 82 " --> pdb=" O THR C 231 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1800 1.34 - 1.46: 881 1.46 - 1.57: 2788 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 5493 Sorted by residual: bond pdb=" CA VAL A 184 " pdb=" CB VAL A 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 6.07e-01 bond pdb=" CA VAL B 184 " pdb=" CB VAL B 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 5.94e-01 bond pdb=" CA VAL C 184 " pdb=" CB VAL C 184 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 4.80e-01 bond pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 1.520 1.527 -0.008 1.16e-02 7.43e+03 4.21e-01 bond pdb=" CA THR B 205 " pdb=" C THR B 205 " ideal model delta sigma weight residual 1.520 1.527 -0.007 1.16e-02 7.43e+03 3.82e-01 ... (remaining 5488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 6946 0.97 - 1.95: 327 1.95 - 2.92: 79 2.92 - 3.90: 22 3.90 - 4.87: 12 Bond angle restraints: 7386 Sorted by residual: angle pdb=" N GLN A 214 " pdb=" CA GLN A 214 " pdb=" C GLN A 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.25e+00 angle pdb=" N GLN B 214 " pdb=" CA GLN B 214 " pdb=" C GLN B 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.24e+00 angle pdb=" N GLN C 214 " pdb=" CA GLN C 214 " pdb=" C GLN C 214 " ideal model delta sigma weight residual 113.20 109.95 3.25 1.21e+00 6.83e-01 7.23e+00 angle pdb=" C GLY A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 122.13 126.13 -4.00 1.85e+00 2.92e-01 4.69e+00 angle pdb=" C GLY B 183 " pdb=" N VAL B 184 " pdb=" CA VAL B 184 " ideal model delta sigma weight residual 122.13 126.08 -3.95 1.85e+00 2.92e-01 4.56e+00 ... (remaining 7381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.58: 2712 10.58 - 21.15: 400 21.15 - 31.73: 179 31.73 - 42.31: 48 42.31 - 52.89: 27 Dihedral angle restraints: 3366 sinusoidal: 1356 harmonic: 2010 Sorted by residual: dihedral pdb=" CA THR C 187 " pdb=" C THR C 187 " pdb=" N PRO C 188 " pdb=" CA PRO C 188 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 187 " pdb=" C THR A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 519 0.030 - 0.059: 192 0.059 - 0.088: 66 0.088 - 0.118: 27 0.118 - 0.147: 3 Chirality restraints: 807 Sorted by residual: chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 804 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 61 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.014 5.00e-02 4.00e+02 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1888 2.86 - 3.37: 4829 3.37 - 3.88: 8252 3.88 - 4.39: 9508 4.39 - 4.90: 16951 Nonbonded interactions: 41428 Sorted by model distance: nonbonded pdb=" NZ LYS A 61 " pdb=" O ASN C 234 " model vdw 2.350 3.120 nonbonded pdb=" O ASN A 234 " pdb=" NZ LYS B 61 " model vdw 2.381 3.120 nonbonded pdb=" O THR B 43 " pdb=" N SER B 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR A 43 " pdb=" N SER A 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR C 43 " pdb=" N SER C 77 " model vdw 2.459 3.120 ... (remaining 41423 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 'B' 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.002 0.018 5493 Z= 0.139 Angle : 0.544 4.871 7386 Z= 0.302 Chirality : 0.038 0.147 807 Planarity : 0.002 0.026 978 Dihedral : 13.406 52.885 2070 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.30 (0.31), residues: 693 helix: -0.42 (0.55), residues: 102 sheet: 0.57 (0.44), residues: 156 loop : -1.60 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 233 HIS 0.000 0.000 HIS C 256 PHE 0.003 0.001 PHE A 109 TYR 0.007 0.001 TYR B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.640 Fit side-chains REVERT: B 33 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7434 (ttpt) REVERT: B 258 GLU cc_start: 0.7546 (pt0) cc_final: 0.7115 (pt0) REVERT: C 155 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8382 (mtmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1752 time to fit residues: 25.3499 Evaluate side-chains 73 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.0070 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 242 HIS C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5493 Z= 0.116 Angle : 0.479 4.680 7386 Z= 0.256 Chirality : 0.039 0.143 807 Planarity : 0.003 0.022 978 Dihedral : 3.795 16.005 714 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.85 % Allowed : 10.15 % Favored : 89.00 % 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: -0.87 (0.31), residues: 693 helix: 1.10 (0.59), residues: 81 sheet: 0.68 (0.42), residues: 159 loop : -1.46 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 233 HIS 0.000 0.000 HIS B 242 PHE 0.004 0.000 PHE B 109 TYR 0.004 0.001 TYR A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 33 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7327 (ttpt) REVERT: B 91 ASP cc_start: 0.7928 (t0) cc_final: 0.7635 (t0) REVERT: B 232 GLN cc_start: 0.8341 (pp30) cc_final: 0.7951 (pp30) REVERT: B 248 TYR cc_start: 0.7834 (t80) cc_final: 0.7213 (t80) REVERT: C 225 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6423 (mt0) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1652 time to fit residues: 22.0090 Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5493 Z= 0.322 Angle : 0.594 6.361 7386 Z= 0.312 Chirality : 0.042 0.171 807 Planarity : 0.003 0.027 978 Dihedral : 4.521 16.655 714 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.03 % Allowed : 12.69 % Favored : 85.28 % 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: -1.37 (0.30), residues: 693 helix: -0.29 (0.51), residues: 102 sheet: 0.81 (0.42), residues: 159 loop : -1.86 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 233 HIS 0.001 0.001 HIS C 242 PHE 0.010 0.001 PHE C 200 TYR 0.016 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 91 ASP cc_start: 0.7975 (t0) cc_final: 0.7611 (t0) REVERT: B 212 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (mtt) REVERT: B 225 GLN cc_start: 0.7289 (tp40) cc_final: 0.7031 (mt0) REVERT: B 248 TYR cc_start: 0.8222 (t80) cc_final: 0.7707 (t80) REVERT: C 193 GLN cc_start: 0.7591 (mt0) cc_final: 0.7266 (mm-40) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.1405 time to fit residues: 16.1442 Evaluate side-chains 72 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5493 Z= 0.147 Angle : 0.499 4.977 7386 Z= 0.264 Chirality : 0.039 0.151 807 Planarity : 0.003 0.025 978 Dihedral : 4.031 17.911 714 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.18 % Allowed : 15.74 % Favored : 83.08 % 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: -0.98 (0.30), residues: 693 helix: 0.98 (0.56), residues: 84 sheet: 0.76 (0.42), residues: 159 loop : -1.61 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 242 PHE 0.005 0.001 PHE C 109 TYR 0.015 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: B 212 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7485 (mtt) REVERT: B 248 TYR cc_start: 0.8231 (t80) cc_final: 0.7885 (t80) REVERT: C 33 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8123 (mmtm) REVERT: C 193 GLN cc_start: 0.7552 (mt0) cc_final: 0.7257 (mm-40) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.1406 time to fit residues: 15.4028 Evaluate side-chains 69 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5493 Z= 0.218 Angle : 0.526 5.199 7386 Z= 0.279 Chirality : 0.040 0.158 807 Planarity : 0.003 0.026 978 Dihedral : 4.134 16.409 714 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.38 % Allowed : 14.55 % Favored : 82.06 % 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: -1.01 (0.31), residues: 693 helix: 1.04 (0.55), residues: 84 sheet: 0.79 (0.42), residues: 159 loop : -1.68 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.029 0.001 PHE C 92 TYR 0.018 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.678 Fit side-chains REVERT: A 111 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 212 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: B 248 TYR cc_start: 0.8259 (t80) cc_final: 0.7852 (t80) REVERT: C 193 GLN cc_start: 0.7548 (mt0) cc_final: 0.7298 (mm-40) outliers start: 20 outliers final: 13 residues processed: 82 average time/residue: 0.1475 time to fit residues: 16.7043 Evaluate side-chains 74 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5493 Z= 0.200 Angle : 0.515 5.113 7386 Z= 0.272 Chirality : 0.040 0.157 807 Planarity : 0.003 0.025 978 Dihedral : 4.106 17.218 714 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.94 % Rotamer: Outliers : 3.05 % Allowed : 15.91 % Favored : 81.05 % 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: -1.02 (0.31), residues: 693 helix: 1.04 (0.56), residues: 84 sheet: 0.77 (0.42), residues: 159 loop : -1.68 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.022 0.001 PHE C 92 TYR 0.016 0.001 TYR B 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.652 Fit side-chains REVERT: A 111 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 212 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: B 248 TYR cc_start: 0.8265 (t80) cc_final: 0.7824 (t80) REVERT: C 193 GLN cc_start: 0.7516 (mt0) cc_final: 0.7299 (mm-40) REVERT: C 196 MET cc_start: 0.7669 (ttm) cc_final: 0.7436 (ttm) outliers start: 18 outliers final: 14 residues processed: 79 average time/residue: 0.1482 time to fit residues: 16.1693 Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5493 Z= 0.254 Angle : 0.546 5.338 7386 Z= 0.288 Chirality : 0.041 0.162 807 Planarity : 0.003 0.025 978 Dihedral : 4.285 16.454 714 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.92 % Rotamer: Outliers : 3.55 % Allowed : 16.41 % Favored : 80.03 % 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: -1.12 (0.31), residues: 693 helix: 1.04 (0.55), residues: 84 sheet: 0.70 (0.42), residues: 159 loop : -1.77 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.023 0.001 PHE C 92 TYR 0.015 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 212 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7702 (mtt) REVERT: B 248 TYR cc_start: 0.8238 (t80) cc_final: 0.7606 (t80) REVERT: C 193 GLN cc_start: 0.7637 (mt0) cc_final: 0.7412 (mm-40) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.1428 time to fit residues: 16.1551 Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.0050 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.0010 chunk 52 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5493 Z= 0.138 Angle : 0.498 8.184 7386 Z= 0.258 Chirality : 0.039 0.154 807 Planarity : 0.002 0.025 978 Dihedral : 3.913 17.670 714 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.09 % Rotamer: Outliers : 3.38 % Allowed : 16.75 % Favored : 79.86 % 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: -1.03 (0.31), residues: 693 helix: 1.16 (0.55), residues: 84 sheet: 0.69 (0.42), residues: 159 loop : -1.69 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.000 0.000 HIS C 256 PHE 0.016 0.001 PHE C 92 TYR 0.015 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.584 Fit side-chains REVERT: A 111 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 225 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6875 (mm-40) REVERT: A 232 GLN cc_start: 0.8699 (pp30) cc_final: 0.7692 (pp30) REVERT: B 194 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8251 (p) REVERT: B 212 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: B 240 LYS cc_start: 0.6845 (tppt) cc_final: 0.6460 (tppt) REVERT: B 248 TYR cc_start: 0.8143 (t80) cc_final: 0.7629 (t80) REVERT: C 193 GLN cc_start: 0.7508 (mt0) cc_final: 0.7272 (mm-40) REVERT: C 196 MET cc_start: 0.7488 (ttm) cc_final: 0.7259 (ttm) outliers start: 20 outliers final: 11 residues processed: 83 average time/residue: 0.1433 time to fit residues: 16.5181 Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5493 Z= 0.185 Angle : 0.511 5.494 7386 Z= 0.268 Chirality : 0.040 0.152 807 Planarity : 0.003 0.026 978 Dihedral : 4.010 16.375 714 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 2.88 % Allowed : 17.09 % Favored : 80.03 % 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: -1.09 (0.31), residues: 693 helix: 1.13 (0.55), residues: 84 sheet: 0.66 (0.42), residues: 159 loop : -1.74 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.018 0.001 PHE C 92 TYR 0.019 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.625 Fit side-chains REVERT: A 111 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 212 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7656 (mtt) REVERT: B 248 TYR cc_start: 0.8205 (t80) cc_final: 0.7687 (t80) REVERT: C 193 GLN cc_start: 0.7559 (mt0) cc_final: 0.7353 (mm-40) outliers start: 17 outliers final: 13 residues processed: 76 average time/residue: 0.1447 time to fit residues: 15.2704 Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5493 Z= 0.247 Angle : 0.550 7.536 7386 Z= 0.286 Chirality : 0.041 0.159 807 Planarity : 0.003 0.027 978 Dihedral : 4.273 16.647 714 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 2.88 % Allowed : 17.26 % Favored : 79.86 % 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: -1.18 (0.31), residues: 693 helix: 1.04 (0.55), residues: 84 sheet: 0.64 (0.42), residues: 159 loop : -1.81 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.020 0.001 PHE C 92 TYR 0.019 0.002 TYR A 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.638 Fit side-chains REVERT: A 111 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 212 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7725 (mtt) REVERT: B 248 TYR cc_start: 0.8256 (t80) cc_final: 0.7671 (t80) REVERT: C 193 GLN cc_start: 0.7564 (mt0) cc_final: 0.7347 (mm-40) outliers start: 17 outliers final: 12 residues processed: 72 average time/residue: 0.1546 time to fit residues: 15.4603 Evaluate side-chains 74 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.105593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090077 restraints weight = 9519.267| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.76 r_work: 0.3014 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5493 Z= 0.305 Angle : 0.588 6.826 7386 Z= 0.307 Chirality : 0.042 0.162 807 Planarity : 0.003 0.031 978 Dihedral : 4.550 16.314 714 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.37 % Favored : 91.49 % Rotamer: Outliers : 2.71 % Allowed : 17.43 % Favored : 79.86 % 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: -1.29 (0.31), residues: 693 helix: 1.02 (0.54), residues: 84 sheet: 0.55 (0.43), residues: 159 loop : -1.90 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 233 HIS 0.002 0.001 HIS C 256 PHE 0.019 0.001 PHE C 92 TYR 0.017 0.002 TYR A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.98 seconds wall clock time: 27 minutes 9.44 seconds (1629.44 seconds total)