Starting phenix.real_space_refine on Sat May 10 06:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.map" model { file = "/net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aur_15673/05_2025/8aur_15673.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3390 2.51 5 N 894 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.66, per 1000 atoms: 0.68 Number of scatterers: 5409 At special positions: 0 Unit cell: (64.428, 72.072, 220.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1113 8.00 N 894 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 677.2 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: 0.50 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: 1.11 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1800 1.34 - 1.46: 881 1.46 - 1.57: 2788 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 5493 Sorted by residual: bond pdb=" CA VAL A 184 " pdb=" CB VAL A 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 6.07e-01 bond pdb=" CA VAL B 184 " pdb=" CB VAL B 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 5.94e-01 bond pdb=" CA VAL C 184 " pdb=" CB VAL C 184 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 4.80e-01 bond pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 1.520 1.527 -0.008 1.16e-02 7.43e+03 4.21e-01 bond pdb=" CA THR B 205 " pdb=" C THR B 205 " ideal model delta sigma weight residual 1.520 1.527 -0.007 1.16e-02 7.43e+03 3.82e-01 ... (remaining 5488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 6946 0.97 - 1.95: 327 1.95 - 2.92: 79 2.92 - 3.90: 22 3.90 - 4.87: 12 Bond angle restraints: 7386 Sorted by residual: angle pdb=" N GLN A 214 " pdb=" CA GLN A 214 " pdb=" C GLN A 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.25e+00 angle pdb=" N GLN B 214 " pdb=" CA GLN B 214 " pdb=" C GLN B 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.24e+00 angle pdb=" N GLN C 214 " pdb=" CA GLN C 214 " pdb=" C GLN C 214 " ideal model delta sigma weight residual 113.20 109.95 3.25 1.21e+00 6.83e-01 7.23e+00 angle pdb=" C GLY A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 122.13 126.13 -4.00 1.85e+00 2.92e-01 4.69e+00 angle pdb=" C GLY B 183 " pdb=" N VAL B 184 " pdb=" CA VAL B 184 " ideal model delta sigma weight residual 122.13 126.08 -3.95 1.85e+00 2.92e-01 4.56e+00 ... (remaining 7381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.58: 2712 10.58 - 21.15: 400 21.15 - 31.73: 179 31.73 - 42.31: 48 42.31 - 52.89: 27 Dihedral angle restraints: 3366 sinusoidal: 1356 harmonic: 2010 Sorted by residual: dihedral pdb=" CA THR C 187 " pdb=" C THR C 187 " pdb=" N PRO C 188 " pdb=" CA PRO C 188 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 187 " pdb=" C THR A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 519 0.030 - 0.059: 192 0.059 - 0.088: 66 0.088 - 0.118: 27 0.118 - 0.147: 3 Chirality restraints: 807 Sorted by residual: chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 804 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 61 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.014 5.00e-02 4.00e+02 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1888 2.86 - 3.37: 4829 3.37 - 3.88: 8252 3.88 - 4.39: 9508 4.39 - 4.90: 16951 Nonbonded interactions: 41428 Sorted by model distance: nonbonded pdb=" NZ LYS A 61 " pdb=" O ASN C 234 " model vdw 2.350 3.120 nonbonded pdb=" O ASN A 234 " pdb=" NZ LYS B 61 " model vdw 2.381 3.120 nonbonded pdb=" O THR B 43 " pdb=" N SER B 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR A 43 " pdb=" N SER A 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR C 43 " pdb=" N SER C 77 " model vdw 2.459 3.120 ... (remaining 41423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.670 Find NCS groups from input model: 0.100 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- 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= 0.107 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 Details of bonding type rmsd hydrogen bonds : bond 0.22586 ( 143) hydrogen bonds : angle 7.86361 ( 363) covalent geometry : bond 0.00212 ( 5493) covalent geometry : angle 0.54447 ( 7386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.719 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: 0.1767 time to fit residues: 25.7273 Evaluate side-chains 73 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.0070 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 242 HIS C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098339 restraints weight = 9139.160| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.94 r_work: 0.3167 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5493 Z= 0.093 Angle : 0.479 4.680 7386 Z= 0.256 Chirality : 0.039 0.143 807 Planarity : 0.003 0.022 978 Dihedral : 3.795 16.005 714 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.85 % Allowed : 10.15 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 693 helix: 1.10 (0.59), residues: 81 sheet: 0.68 (0.42), residues: 159 loop : -1.46 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 233 HIS 0.000 0.000 HIS B 242 PHE 0.004 0.000 PHE B 109 TYR 0.004 0.001 TYR A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 143) hydrogen bonds : angle 5.43455 ( 363) covalent geometry : bond 0.00181 ( 5493) covalent geometry : angle 0.47872 ( 7386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: B 33 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7288 (ttpt) REVERT: B 91 ASP cc_start: 0.8220 (t0) cc_final: 0.7883 (t0) REVERT: B 232 GLN cc_start: 0.8745 (pp30) cc_final: 0.8143 (pp30) REVERT: B 248 TYR cc_start: 0.7793 (t80) cc_final: 0.6798 (t80) REVERT: C 45 ASP cc_start: 0.8026 (m-30) cc_final: 0.7726 (t0) REVERT: C 50 GLU cc_start: 0.8079 (tp30) cc_final: 0.7742 (tp30) REVERT: C 155 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8781 (ttpp) REVERT: C 225 GLN cc_start: 0.7306 (mm-40) cc_final: 0.6866 (mt0) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1605 time to fit residues: 21.4946 Evaluate side-chains 81 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 C 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095148 restraints weight = 9303.095| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.84 r_work: 0.3025 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5493 Z= 0.126 Angle : 0.513 5.874 7386 Z= 0.269 Chirality : 0.040 0.155 807 Planarity : 0.003 0.023 978 Dihedral : 3.964 15.971 714 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.51 % Allowed : 13.03 % Favored : 86.46 % 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: -1.24 (0.30), residues: 693 helix: -0.21 (0.51), residues: 102 sheet: 0.81 (0.43), residues: 159 loop : -1.72 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 233 HIS 0.001 0.000 HIS C 242 PHE 0.008 0.001 PHE C 200 TYR 0.016 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 143) hydrogen bonds : angle 5.13134 ( 363) covalent geometry : bond 0.00289 ( 5493) covalent geometry : angle 0.51314 ( 7386) *********************** 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 86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: B 91 ASP cc_start: 0.8209 (t0) cc_final: 0.7976 (t0) REVERT: B 212 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: B 248 TYR cc_start: 0.8042 (t80) cc_final: 0.7032 (t80) REVERT: C 45 ASP cc_start: 0.8039 (m-30) cc_final: 0.7791 (t0) REVERT: C 50 GLU cc_start: 0.8036 (tp30) cc_final: 0.7671 (tp30) REVERT: C 113 LEU cc_start: 0.8576 (pp) cc_final: 0.8356 (pp) REVERT: C 151 GLU cc_start: 0.8170 (tp30) cc_final: 0.7947 (tp30) REVERT: C 193 GLN cc_start: 0.7800 (mt0) cc_final: 0.7319 (mm-40) REVERT: C 225 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6721 (mt0) outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 0.1465 time to fit residues: 17.0985 Evaluate side-chains 67 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.0070 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.0000 overall best weight: 0.3804 ------------------------------------------------------------------------------- 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 C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095173 restraints weight = 9551.024| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.93 r_work: 0.3103 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5493 Z= 0.100 Angle : 0.484 4.906 7386 Z= 0.254 Chirality : 0.039 0.151 807 Planarity : 0.002 0.023 978 Dihedral : 3.796 16.530 714 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.35 % Allowed : 14.72 % Favored : 83.93 % 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: -0.84 (0.31), residues: 693 helix: 0.91 (0.56), residues: 87 sheet: 0.83 (0.42), residues: 159 loop : -1.48 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 233 HIS 0.001 0.000 HIS C 242 PHE 0.006 0.001 PHE C 109 TYR 0.014 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 143) hydrogen bonds : angle 4.78303 ( 363) covalent geometry : bond 0.00222 ( 5493) covalent geometry : angle 0.48446 ( 7386) *********************** 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 80 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.596 Fit side-chains REVERT: A 111 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 91 ASP cc_start: 0.8143 (t0) cc_final: 0.7880 (t0) REVERT: B 212 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7454 (mtt) REVERT: B 248 TYR cc_start: 0.8079 (t80) cc_final: 0.7199 (t80) REVERT: C 33 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8017 (mmtm) REVERT: C 118 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7979 (mmtt) REVERT: C 193 GLN cc_start: 0.7850 (mt0) cc_final: 0.7428 (mm-40) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.1305 time to fit residues: 14.6443 Evaluate side-chains 74 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090066 restraints weight = 9557.707| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2940 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5493 Z= 0.249 Angle : 0.618 7.058 7386 Z= 0.325 Chirality : 0.043 0.176 807 Planarity : 0.003 0.026 978 Dihedral : 4.673 15.851 714 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.88 % Allowed : 14.04 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.30), residues: 693 helix: -0.29 (0.51), residues: 105 sheet: 0.77 (0.42), residues: 159 loop : -1.88 (0.27), residues: 429 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 0.032 0.002 PHE C 92 TYR 0.017 0.002 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 143) hydrogen bonds : angle 5.41054 ( 363) covalent geometry : bond 0.00587 ( 5493) covalent geometry : angle 0.61755 ( 7386) *********************** 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 80 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.652 Fit side-chains REVERT: A 111 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 91 ASP cc_start: 0.8344 (t0) cc_final: 0.7821 (t0) REVERT: B 203 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7520 (t0) REVERT: B 212 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7843 (mtt) REVERT: B 248 TYR cc_start: 0.8209 (t80) cc_final: 0.7431 (t80) REVERT: C 118 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8007 (tppt) REVERT: C 201 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7915 (ptmt) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.1498 time to fit residues: 16.0088 Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 187 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.091169 restraints weight = 9494.469| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.80 r_work: 0.3011 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3141 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= 0.164 Angle : 0.546 5.272 7386 Z= 0.289 Chirality : 0.041 0.161 807 Planarity : 0.003 0.026 978 Dihedral : 4.380 17.684 714 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.21 % Allowed : 14.72 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 693 helix: 1.03 (0.55), residues: 84 sheet: 0.70 (0.42), residues: 159 loop : -1.73 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.023 0.001 PHE C 92 TYR 0.017 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 143) hydrogen bonds : angle 5.13189 ( 363) covalent geometry : bond 0.00384 ( 5493) covalent geometry : angle 0.54631 ( 7386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.701 Fit side-chains REVERT: A 111 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 91 ASP cc_start: 0.8282 (t0) cc_final: 0.8010 (t0) REVERT: B 212 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7848 (mtt) REVERT: B 248 TYR cc_start: 0.8150 (t80) cc_final: 0.7334 (t80) REVERT: C 118 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7987 (tppt) REVERT: C 151 GLU cc_start: 0.8353 (tp30) cc_final: 0.8120 (tp30) REVERT: C 189 THR cc_start: 0.8028 (m) cc_final: 0.7389 (p) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1392 time to fit residues: 15.5433 Evaluate side-chains 72 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 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 = 0.3360 r_free = 0.3360 target = 0.105097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089351 restraints weight = 9616.285| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.87 r_work: 0.2981 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3287 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= 0.178 Angle : 0.554 5.402 7386 Z= 0.293 Chirality : 0.041 0.163 807 Planarity : 0.003 0.029 978 Dihedral : 4.371 16.336 714 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.37 % Favored : 91.49 % Rotamer: Outliers : 4.06 % Allowed : 14.72 % Favored : 81.22 % 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: -1.14 (0.31), residues: 693 helix: 1.07 (0.55), residues: 84 sheet: 0.67 (0.42), residues: 159 loop : -1.78 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.022 0.001 PHE C 92 TYR 0.016 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 143) hydrogen bonds : angle 5.14973 ( 363) covalent geometry : bond 0.00418 ( 5493) covalent geometry : angle 0.55426 ( 7386) *********************** 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 82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 212 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: B 248 TYR cc_start: 0.8110 (t80) cc_final: 0.7136 (t80) REVERT: C 49 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8534 (tppt) REVERT: C 196 MET cc_start: 0.8528 (ttm) cc_final: 0.8164 (ttm) REVERT: C 201 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7943 (ptmt) outliers start: 24 outliers final: 18 residues processed: 77 average time/residue: 0.1504 time to fit residues: 15.9461 Evaluate side-chains 82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.106969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091371 restraints weight = 9496.650| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.81 r_work: 0.3045 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3304 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= 0.135 Angle : 0.529 7.167 7386 Z= 0.276 Chirality : 0.040 0.160 807 Planarity : 0.003 0.025 978 Dihedral : 4.172 17.187 714 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 3.55 % Allowed : 15.57 % Favored : 80.88 % 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: -1.07 (0.31), residues: 693 helix: 1.17 (0.55), residues: 84 sheet: 0.67 (0.43), residues: 159 loop : -1.73 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.019 0.001 PHE C 92 TYR 0.015 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 143) hydrogen bonds : angle 4.95568 ( 363) covalent geometry : bond 0.00314 ( 5493) covalent geometry : angle 0.52900 ( 7386) *********************** 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 90 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.624 Fit side-chains REVERT: A 111 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 139 TYR cc_start: 0.8587 (t80) cc_final: 0.8357 (t80) REVERT: B 212 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7901 (mtt) REVERT: B 248 TYR cc_start: 0.8178 (t80) cc_final: 0.7197 (t80) REVERT: C 49 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8518 (tppt) REVERT: C 118 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (tppt) REVERT: C 151 GLU cc_start: 0.8401 (tp30) cc_final: 0.8152 (tp30) REVERT: C 196 MET cc_start: 0.8400 (ttm) cc_final: 0.8094 (ttm) outliers start: 21 outliers final: 17 residues processed: 84 average time/residue: 0.1334 time to fit residues: 15.7962 Evaluate side-chains 84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 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 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 11 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.108201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092675 restraints weight = 9410.284| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.79 r_work: 0.3052 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3333 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= 0.119 Angle : 0.520 8.225 7386 Z= 0.270 Chirality : 0.039 0.150 807 Planarity : 0.003 0.030 978 Dihedral : 4.035 16.783 714 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.93 % Favored : 92.93 % Rotamer: Outliers : 3.55 % Allowed : 16.07 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 693 helix: 1.20 (0.55), residues: 84 sheet: 0.64 (0.43), residues: 159 loop : -1.74 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.017 0.001 PHE C 92 TYR 0.015 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 143) hydrogen bonds : angle 4.85220 ( 363) covalent geometry : bond 0.00273 ( 5493) covalent geometry : angle 0.52038 ( 7386) *********************** 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 88 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.634 Fit side-chains REVERT: A 111 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 139 TYR cc_start: 0.8594 (t80) cc_final: 0.8382 (t80) REVERT: A 232 GLN cc_start: 0.8927 (pp30) cc_final: 0.7717 (pp30) REVERT: B 212 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: B 248 TYR cc_start: 0.8197 (t80) cc_final: 0.7330 (t80) REVERT: C 49 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8583 (tppt) REVERT: C 118 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7984 (tppt) REVERT: C 151 GLU cc_start: 0.8371 (tp30) cc_final: 0.8107 (tp30) REVERT: C 193 GLN cc_start: 0.8105 (mt0) cc_final: 0.7867 (mm-40) REVERT: C 196 MET cc_start: 0.8327 (ttm) cc_final: 0.8046 (ttm) outliers start: 21 outliers final: 17 residues processed: 81 average time/residue: 0.1390 time to fit residues: 16.5130 Evaluate side-chains 85 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 177 THR 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 73 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091169 restraints weight = 9597.193| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.83 r_work: 0.3041 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3404 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= 0.148 Angle : 0.547 8.401 7386 Z= 0.285 Chirality : 0.040 0.155 807 Planarity : 0.003 0.028 978 Dihedral : 4.178 16.418 714 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 3.89 % Allowed : 15.74 % Favored : 80.37 % 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: -1.13 (0.31), residues: 693 helix: 1.21 (0.55), residues: 84 sheet: 0.62 (0.43), residues: 159 loop : -1.78 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.018 0.001 PHE C 92 TYR 0.014 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 143) hydrogen bonds : angle 4.95367 ( 363) covalent geometry : bond 0.00346 ( 5493) covalent geometry : angle 0.54702 ( 7386) ********************** 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 89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.710 Fit side-chains REVERT: A 111 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 139 TYR cc_start: 0.8606 (t80) cc_final: 0.8402 (t80) REVERT: B 212 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: B 248 TYR cc_start: 0.8201 (t80) cc_final: 0.7293 (t80) REVERT: C 49 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8536 (tppt) REVERT: C 118 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8003 (tppt) REVERT: C 151 GLU cc_start: 0.8398 (tp30) cc_final: 0.8156 (tp30) REVERT: C 196 MET cc_start: 0.8410 (ttm) cc_final: 0.8156 (ttm) outliers start: 23 outliers final: 19 residues processed: 82 average time/residue: 0.1361 time to fit residues: 15.6529 Evaluate side-chains 85 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 THR 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 73 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.0060 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.106967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091249 restraints weight = 9565.283| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.87 r_work: 0.2998 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5493 Z= 0.130 Angle : 0.533 8.088 7386 Z= 0.280 Chirality : 0.040 0.153 807 Planarity : 0.003 0.031 978 Dihedral : 4.090 16.794 714 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 3.72 % Allowed : 15.91 % Favored : 80.37 % 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: -1.11 (0.31), residues: 693 helix: 1.21 (0.55), residues: 84 sheet: 0.65 (0.43), residues: 159 loop : -1.77 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.018 0.001 PHE C 92 TYR 0.014 0.001 TYR A 89 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 143) hydrogen bonds : angle 4.86851 ( 363) covalent geometry : bond 0.00299 ( 5493) covalent geometry : angle 0.53326 ( 7386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.35 seconds wall clock time: 41 minutes 42.70 seconds (2502.70 seconds total)