Starting phenix.real_space_refine on Tue Feb 13 10:33:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_2024/8aur_15673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_2024/8aur_15673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_2024/8aur_15673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_2024/8aur_15673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aur_15673/02_2024/8aur_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-dev-5238/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: 3.35, per 1000 atoms: 0.62 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: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.53 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: 1.22 Time building geometry restraints manager: 2.21 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: 1.590 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: 0.000 Extract box with map and model: 4.660 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.470 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- 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 : 0.656 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: 0.1739 time to fit residues: 25.2222 Evaluate side-chains 73 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 4.9990 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 242 HIS C 156 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1918 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= 0.209 Angle : 0.521 5.116 7386 Z= 0.278 Chirality : 0.040 0.157 807 Planarity : 0.003 0.025 978 Dihedral : 4.166 16.404 714 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.18 % Allowed : 10.66 % Favored : 88.16 % 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: -0.39 (0.51), residues: 102 sheet: 0.73 (0.43), residues: 159 loop : -1.68 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 233 HIS 0.001 0.000 HIS C 256 PHE 0.008 0.001 PHE C 200 TYR 0.006 0.001 TYR A 89 *********************** 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 84 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.620 Fit side-chains REVERT: B 91 ASP cc_start: 0.7983 (t0) cc_final: 0.7712 (t0) REVERT: B 225 GLN cc_start: 0.7342 (tp40) cc_final: 0.7137 (mt0) REVERT: B 248 TYR cc_start: 0.8130 (t80) cc_final: 0.7562 (t80) REVERT: C 225 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6443 (mt0) outliers start: 7 outliers final: 6 residues processed: 82 average time/residue: 0.1495 time to fit residues: 16.8097 Evaluate side-chains 76 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 55 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2393 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= 0.203 Angle : 0.510 5.344 7386 Z= 0.269 Chirality : 0.040 0.158 807 Planarity : 0.003 0.025 978 Dihedral : 4.105 17.050 714 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.20 % Allowed : 14.38 % 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: -0.95 (0.31), residues: 693 helix: 0.93 (0.56), residues: 81 sheet: 0.85 (0.43), residues: 159 loop : -1.60 (0.27), residues: 453 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 0.006 0.001 PHE C 200 TYR 0.008 0.001 TYR B 124 *********************** 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 81 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.682 Fit side-chains REVERT: A 111 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8389 (p) REVERT: B 91 ASP cc_start: 0.7949 (t0) cc_final: 0.7541 (t0) REVERT: B 212 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7550 (mtt) REVERT: B 225 GLN cc_start: 0.7435 (tp40) cc_final: 0.7117 (mt0) REVERT: B 248 TYR cc_start: 0.8264 (t80) cc_final: 0.7819 (t80) REVERT: C 193 GLN cc_start: 0.7462 (mt0) cc_final: 0.7195 (mm-40) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1491 time to fit residues: 16.4216 Evaluate side-chains 75 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 187 THR 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 51 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 243 THR 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: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5493 Z= 0.355 Angle : 0.611 7.799 7386 Z= 0.318 Chirality : 0.042 0.172 807 Planarity : 0.003 0.028 978 Dihedral : 4.683 16.288 714 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.89 % Allowed : 14.72 % Favored : 81.39 % 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: -1.45 (0.31), residues: 693 helix: -0.42 (0.50), residues: 102 sheet: 0.77 (0.42), residues: 159 loop : -1.91 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 233 HIS 0.002 0.001 HIS C 242 PHE 0.035 0.002 PHE C 92 TYR 0.010 0.001 TYR A 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 85 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.660 Fit side-chains REVERT: A 111 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 212 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: B 248 TYR cc_start: 0.8225 (t80) cc_final: 0.7727 (t80) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 0.1450 time to fit residues: 16.0641 Evaluate side-chains 72 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain B residue 173 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 38 THR Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 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: 0.8980 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3015 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= 0.207 Angle : 0.521 6.122 7386 Z= 0.273 Chirality : 0.040 0.160 807 Planarity : 0.003 0.025 978 Dihedral : 4.261 18.119 714 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.72 % Allowed : 15.74 % 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: -1.10 (0.31), residues: 693 helix: 1.03 (0.55), residues: 81 sheet: 0.75 (0.43), residues: 159 loop : -1.75 (0.28), residues: 453 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 0.020 0.001 PHE C 92 TYR 0.007 0.001 TYR B 124 *********************** 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 81 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.676 Fit side-chains REVERT: A 139 TYR cc_start: 0.8527 (t80) cc_final: 0.8268 (t80) REVERT: B 212 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: B 248 TYR cc_start: 0.8067 (t80) cc_final: 0.7573 (t80) outliers start: 22 outliers final: 17 residues processed: 77 average time/residue: 0.1357 time to fit residues: 14.7713 Evaluate side-chains 76 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER 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 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 51 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5493 Z= 0.233 Angle : 0.539 6.138 7386 Z= 0.280 Chirality : 0.040 0.158 807 Planarity : 0.003 0.026 978 Dihedral : 4.263 16.824 714 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.55 % Allowed : 16.24 % Favored : 80.20 % 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: -1.16 (0.31), residues: 693 helix: 0.95 (0.54), residues: 81 sheet: 0.76 (0.43), residues: 159 loop : -1.80 (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 256 PHE 0.018 0.001 PHE C 92 TYR 0.008 0.001 TYR C 139 *********************** 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 82 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.677 Fit side-chains REVERT: B 91 ASP cc_start: 0.7961 (t0) cc_final: 0.7749 (t0) REVERT: B 212 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7632 (mtt) REVERT: B 248 TYR cc_start: 0.8080 (t80) cc_final: 0.7533 (t80) outliers start: 21 outliers final: 18 residues processed: 79 average time/residue: 0.1427 time to fit residues: 15.6900 Evaluate side-chains 77 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER 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 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 51 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5493 Z= 0.178 Angle : 0.506 5.136 7386 Z= 0.264 Chirality : 0.039 0.156 807 Planarity : 0.003 0.026 978 Dihedral : 4.080 17.482 714 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 2.20 % Allowed : 18.27 % 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: -1.10 (0.31), residues: 693 helix: 1.04 (0.55), residues: 81 sheet: 0.78 (0.43), residues: 159 loop : -1.76 (0.28), residues: 453 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 0.016 0.001 PHE C 92 TYR 0.007 0.001 TYR C 139 *********************** 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 77 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.677 Fit side-chains REVERT: A 139 TYR cc_start: 0.8541 (t80) cc_final: 0.8278 (t80) REVERT: B 212 MET cc_start: 0.7855 (mtp) cc_final: 0.7652 (mtt) REVERT: B 248 TYR cc_start: 0.8056 (t80) cc_final: 0.7491 (t80) REVERT: C 193 GLN cc_start: 0.7625 (mt0) cc_final: 0.7387 (mm-40) outliers start: 13 outliers final: 13 residues processed: 76 average time/residue: 0.1391 time to fit residues: 14.8906 Evaluate side-chains 73 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 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 C residue 38 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 overall best weight: 0.6042 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.3243 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= 0.187 Angle : 0.509 5.746 7386 Z= 0.265 Chirality : 0.039 0.154 807 Planarity : 0.003 0.027 978 Dihedral : 4.010 17.032 714 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 2.88 % Allowed : 18.95 % Favored : 78.17 % 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: -1.10 (0.31), residues: 693 helix: 1.13 (0.55), residues: 81 sheet: 0.75 (0.43), residues: 159 loop : -1.77 (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 256 PHE 0.014 0.001 PHE C 92 TYR 0.007 0.001 TYR C 139 *********************** 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 79 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.664 Fit side-chains REVERT: A 139 TYR cc_start: 0.8546 (t80) cc_final: 0.8315 (t80) REVERT: B 248 TYR cc_start: 0.8061 (t80) cc_final: 0.7439 (t80) REVERT: C 193 GLN cc_start: 0.7664 (mt0) cc_final: 0.7438 (mm-40) outliers start: 17 outliers final: 16 residues processed: 76 average time/residue: 0.1428 time to fit residues: 15.2755 Evaluate side-chains 75 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER 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 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 C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR 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: 0.0470 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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: 0.8096 moved from start: 0.3362 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= 0.256 Angle : 0.553 6.757 7386 Z= 0.286 Chirality : 0.040 0.161 807 Planarity : 0.003 0.028 978 Dihedral : 4.253 16.729 714 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.23 % Favored : 91.63 % Rotamer: Outliers : 3.55 % Allowed : 18.27 % Favored : 78.17 % 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: -1.20 (0.31), residues: 693 helix: 1.04 (0.54), residues: 81 sheet: 0.70 (0.43), residues: 159 loop : -1.84 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.015 0.001 PHE C 92 TYR 0.008 0.001 TYR A 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 76 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.725 Fit side-chains REVERT: A 139 TYR cc_start: 0.8580 (t80) cc_final: 0.8364 (t80) REVERT: B 248 TYR cc_start: 0.8106 (t80) cc_final: 0.7561 (t80) outliers start: 21 outliers final: 18 residues processed: 74 average time/residue: 0.1345 time to fit residues: 14.1885 Evaluate side-chains 73 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 173 ILE 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 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 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.8119 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 0.033 5493 Z= 0.315 Angle : 0.589 5.977 7386 Z= 0.306 Chirality : 0.041 0.163 807 Planarity : 0.003 0.029 978 Dihedral : 4.524 17.411 714 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.95 % Favored : 90.91 % Rotamer: Outliers : 3.05 % Allowed : 19.12 % Favored : 77.83 % 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: 0.91 (0.54), residues: 81 sheet: 0.62 (0.43), residues: 159 loop : -1.90 (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 0.014 0.001 PHE C 92 TYR 0.009 0.001 TYR A 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 76 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.613 Fit side-chains REVERT: A 139 TYR cc_start: 0.8584 (t80) cc_final: 0.8376 (t80) REVERT: B 248 TYR cc_start: 0.8076 (t80) cc_final: 0.7489 (t80) outliers start: 18 outliers final: 18 residues processed: 74 average time/residue: 0.1365 time to fit residues: 14.2628 Evaluate side-chains 74 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 173 ILE 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 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 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR 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: 1.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091416 restraints weight = 9472.395| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.80 r_work: 0.3047 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3502 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= 0.222 Angle : 0.544 6.553 7386 Z= 0.283 Chirality : 0.040 0.159 807 Planarity : 0.003 0.027 978 Dihedral : 4.278 17.298 714 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.77 % Rotamer: Outliers : 3.38 % Allowed : 18.61 % Favored : 78.00 % 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: -1.25 (0.31), residues: 693 helix: 1.02 (0.54), residues: 81 sheet: 0.62 (0.44), residues: 159 loop : -1.86 (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 0.014 0.001 PHE C 92 TYR 0.007 0.001 TYR A 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.20 seconds wall clock time: 26 minutes 19.98 seconds (1579.98 seconds total)