Starting phenix.real_space_refine on Thu Dec 7 22:38:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_15673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_15673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_15673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_15673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/12_2023/8aur_15673.pdb" } 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 Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 259": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.06, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 1.92 Conformation dependent library (CDL) restraints added in 927.2 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: 1.13 Time building geometry restraints manager: 2.10 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: 99.19 - 106.14: 93 106.14 - 113.09: 2981 113.09 - 120.04: 1782 120.04 - 126.99: 2497 126.99 - 133.94: 33 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 2.520 nonbonded pdb=" O ASN A 234 " pdb=" NZ LYS B 61 " model vdw 2.381 2.520 nonbonded pdb=" O THR B 43 " pdb=" N SER B 77 " model vdw 2.459 2.520 nonbonded pdb=" O THR A 43 " pdb=" N SER A 77 " model vdw 2.459 2.520 nonbonded pdb=" O THR C 43 " pdb=" N SER C 77 " model vdw 2.459 2.520 ... (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 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: 1.130 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: 4.580 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.607 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1760 time to fit residues: 25.5588 Evaluate side-chains 76 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8923 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 234 ASN B 242 HIS C 156 GLN C 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2009 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= 0.210 Angle : 0.524 5.148 7386 Z= 0.279 Chirality : 0.040 0.157 807 Planarity : 0.003 0.025 978 Dihedral : 4.189 16.475 714 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.02 % Allowed : 11.51 % Favored : 87.48 % 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: -1.28 (0.31), residues: 693 helix: -0.38 (0.52), residues: 102 sheet: 0.74 (0.43), residues: 159 loop : -1.69 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 233 HIS 0.001 0.000 HIS C 256 PHE 0.008 0.001 PHE C 200 TYR 0.006 0.001 TYR C 217 *********************** 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 85 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.631 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.1481 time to fit residues: 17.0641 Evaluate side-chains 80 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0540 time to fit residues: 1.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2477 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= 0.210 Angle : 0.518 5.471 7386 Z= 0.272 Chirality : 0.040 0.159 807 Planarity : 0.003 0.025 978 Dihedral : 4.139 17.051 714 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.35 % Allowed : 15.23 % Favored : 83.42 % 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: -1.26 (0.31), residues: 693 helix: -0.40 (0.51), residues: 102 sheet: 0.88 (0.43), residues: 159 loop : -1.73 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.002 0.000 HIS C 242 PHE 0.007 0.001 PHE C 200 TYR 0.013 0.001 TYR B 248 *********************** 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 84 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.651 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.1453 time to fit residues: 16.5703 Evaluate side-chains 72 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0526 time to fit residues: 1.3735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 215 ASN C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5493 Z= 0.229 Angle : 0.527 5.240 7386 Z= 0.278 Chirality : 0.040 0.160 807 Planarity : 0.003 0.026 978 Dihedral : 4.208 16.974 714 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.35 % Allowed : 15.40 % Favored : 83.25 % 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: -0.94 (0.31), residues: 693 helix: 0.92 (0.55), residues: 81 sheet: 0.87 (0.43), residues: 159 loop : -1.59 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 242 PHE 0.030 0.001 PHE C 92 TYR 0.014 0.001 TYR B 248 *********************** 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 82 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.674 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1491 time to fit residues: 16.6107 Evaluate side-chains 64 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0549 time to fit residues: 1.3563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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: 0.8155 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5493 Z= 0.460 Angle : 0.683 8.092 7386 Z= 0.357 Chirality : 0.044 0.181 807 Planarity : 0.004 0.030 978 Dihedral : 5.086 18.566 714 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.67 % Favored : 90.19 % Rotamer: Outliers : 2.20 % Allowed : 17.09 % Favored : 80.71 % 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: -1.67 (0.31), residues: 693 helix: -0.55 (0.50), residues: 102 sheet: 0.68 (0.42), residues: 159 loop : -2.09 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 233 HIS 0.002 0.001 HIS C 242 PHE 0.010 0.002 PHE B 200 TYR 0.017 0.002 TYR B 248 *********************** 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 70 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.650 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.1465 time to fit residues: 14.1112 Evaluate side-chains 61 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0524 time to fit residues: 1.8782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3235 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= 0.169 Angle : 0.513 5.378 7386 Z= 0.270 Chirality : 0.039 0.158 807 Planarity : 0.003 0.026 978 Dihedral : 4.272 18.193 714 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.80 % Rotamer: Outliers : 0.85 % Allowed : 18.61 % Favored : 80.54 % 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: -1.21 (0.31), residues: 693 helix: 0.94 (0.55), residues: 81 sheet: 0.72 (0.43), residues: 159 loop : -1.84 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS B 256 PHE 0.004 0.001 PHE C 200 TYR 0.011 0.001 TYR B 248 *********************** 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 69 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.618 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.1598 time to fit residues: 15.0191 Evaluate side-chains 60 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1890 time to fit residues: 1.3814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5493 Z= 0.297 Angle : 0.584 7.260 7386 Z= 0.303 Chirality : 0.041 0.169 807 Planarity : 0.003 0.029 978 Dihedral : 4.547 17.301 714 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.38 % Favored : 90.48 % Rotamer: Outliers : 0.34 % Allowed : 20.14 % Favored : 79.53 % 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: -1.34 (0.31), residues: 693 helix: 0.91 (0.55), residues: 81 sheet: 0.68 (0.43), residues: 159 loop : -1.97 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 233 HIS 0.001 0.001 HIS C 256 PHE 0.006 0.001 PHE A 200 TYR 0.012 0.001 TYR B 248 *********************** 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 57 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.657 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.1510 time to fit residues: 12.2175 Evaluate side-chains 55 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0512 time to fit residues: 1.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 6 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5493 Z= 0.233 Angle : 0.543 6.576 7386 Z= 0.284 Chirality : 0.040 0.163 807 Planarity : 0.003 0.030 978 Dihedral : 4.338 17.168 714 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 0.85 % Allowed : 19.80 % Favored : 79.36 % 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: -1.32 (0.31), residues: 693 helix: 1.02 (0.55), residues: 81 sheet: 0.62 (0.43), residues: 159 loop : -1.94 (0.28), residues: 453 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 0.005 0.001 PHE C 200 TYR 0.010 0.001 TYR B 248 *********************** 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 62 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.624 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1548 time to fit residues: 12.9470 Evaluate side-chains 57 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0567 time to fit residues: 1.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.0030 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5493 Z= 0.253 Angle : 0.566 7.846 7386 Z= 0.294 Chirality : 0.041 0.162 807 Planarity : 0.003 0.030 978 Dihedral : 4.395 17.090 714 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.52 % Favored : 90.33 % Rotamer: Outliers : 0.51 % Allowed : 19.97 % Favored : 79.53 % 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: -1.39 (0.31), residues: 693 helix: 0.99 (0.55), residues: 81 sheet: 0.40 (0.42), residues: 165 loop : -1.95 (0.28), residues: 447 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 0.005 0.001 PHE C 200 TYR 0.010 0.001 TYR B 248 *********************** 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 60 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.561 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.1370 time to fit residues: 11.7208 Evaluate side-chains 65 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0540 time to fit residues: 1.1864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5493 Z= 0.228 Angle : 0.552 7.062 7386 Z= 0.288 Chirality : 0.040 0.161 807 Planarity : 0.003 0.029 978 Dihedral : 4.317 17.063 714 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.92 % Rotamer: Outliers : 0.51 % Allowed : 20.81 % Favored : 78.68 % 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: -1.34 (0.31), residues: 693 helix: 1.05 (0.55), residues: 81 sheet: 0.60 (0.43), residues: 159 loop : -1.96 (0.27), residues: 453 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 0.004 0.001 PHE C 200 TYR 0.010 0.001 TYR B 248 ********************** 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 65 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.662 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.1460 time to fit residues: 13.1949 Evaluate side-chains 59 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0590 time to fit residues: 1.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090415 restraints weight = 9477.449| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.84 r_work: 0.3018 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5493 Z= 0.269 Angle : 0.578 7.525 7386 Z= 0.301 Chirality : 0.041 0.163 807 Planarity : 0.003 0.029 978 Dihedral : 4.458 17.805 714 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.38 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 20.98 % Favored : 79.02 % 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: -1.38 (0.31), residues: 693 helix: 1.03 (0.55), residues: 81 sheet: 0.38 (0.42), residues: 165 loop : -1.94 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.005 0.001 PHE C 200 TYR 0.010 0.001 TYR B 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.40 seconds wall clock time: 25 minutes 38.67 seconds (1538.67 seconds total)