Starting phenix.real_space_refine on Wed Mar 5 14:17:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhv_43242/03_2025/8vhv_43242.cif" } resolution = 2.3 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= 0.017 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 11 5.16 5 C 878 2.51 5 N 219 2.21 5 O 227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1335 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Time building chain proxies: 2.59, per 1000 atoms: 1.94 Number of scatterers: 1335 At special positions: 0 Unit cell: (41.85, 51.15, 82.77, 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 11 16.00 O 227 8.00 N 219 7.00 C 878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 39 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 76 " distance=2.02 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: 0.33 Conformation dependent library (CDL) restraints added in 163.0 milliseconds 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 310 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 67.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.720A pdb=" N LEU A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.821A pdb=" N GLN A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 78 removed outlier: 4.082A pdb=" N LEU A 75 " --> pdb=" O CYS A 67 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 303 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: 0.37 Time building geometry restraints manager: 0.41 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: 403 1.34 - 1.46: 301 1.46 - 1.58: 644 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 1365 Sorted by residual: bond pdb=" N ARG A 5 " pdb=" CA ARG A 5 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" C VAL A 142 " pdb=" O VAL A 142 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.12e-02 7.97e+03 4.27e-01 bond pdb=" CA CYS A 66 " pdb=" CB CYS A 66 " ideal model delta sigma weight residual 1.534 1.519 0.016 2.47e-02 1.64e+03 4.00e-01 bond pdb=" C GLU A 69 " pdb=" O GLU A 69 " ideal model delta sigma weight residual 1.232 1.226 0.006 1.01e-02 9.80e+03 3.58e-01 bond pdb=" CA GLU A 190 " pdb=" C GLU A 190 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.30e-02 5.92e+03 3.32e-01 ... (remaining 1360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 1733 1.14 - 2.29: 89 2.29 - 3.43: 11 3.43 - 4.57: 4 4.57 - 5.71: 3 Bond angle restraints: 1840 Sorted by residual: angle pdb=" N PHE A 106 " pdb=" CA PHE A 106 " pdb=" C PHE A 106 " ideal model delta sigma weight residual 109.81 115.52 -5.71 2.21e+00 2.05e-01 6.68e+00 angle pdb=" C ARG A 130 " pdb=" N HIS A 131 " pdb=" CA HIS A 131 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 angle pdb=" N HIS A 131 " pdb=" CA HIS A 131 " pdb=" C HIS A 131 " ideal model delta sigma weight residual 110.80 115.40 -4.60 2.13e+00 2.20e-01 4.67e+00 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 111.19 114.21 -3.02 1.45e+00 4.76e-01 4.32e+00 angle pdb=" N GLU A 69 " pdb=" CA GLU A 69 " pdb=" C GLU A 69 " ideal model delta sigma weight residual 110.06 112.93 -2.87 1.43e+00 4.89e-01 4.02e+00 ... (remaining 1835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.64: 582 8.64 - 17.28: 123 17.28 - 25.92: 42 25.92 - 34.55: 19 34.55 - 43.19: 10 Dihedral angle restraints: 776 sinusoidal: 290 harmonic: 486 Sorted by residual: dihedral pdb=" CA THR A 129 " pdb=" C THR A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N CYS A 120 " pdb=" CA CYS A 120 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE A 106 " pdb=" C PHE A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 773 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 103 0.027 - 0.054: 76 0.054 - 0.080: 22 0.080 - 0.106: 4 0.106 - 0.133: 4 Chirality restraints: 209 Sorted by residual: chirality pdb=" CA PRO A 107 " pdb=" N PRO A 107 " pdb=" C PRO A 107 " pdb=" CB PRO A 107 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA LEU A 68 " pdb=" N LEU A 68 " pdb=" C LEU A 68 " pdb=" CB LEU A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VAL A 56 " pdb=" N VAL A 56 " pdb=" C VAL A 56 " pdb=" CB VAL A 56 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 206 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C SER A 110 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 64 " -0.147 9.50e-02 1.11e+02 6.64e-02 3.14e+00 pdb=" NE ARG A 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 64 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 64 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 64 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 200 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C PHE A 200 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 200 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 201 " -0.010 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 437 2.84 - 3.35: 1365 3.35 - 3.87: 2184 3.87 - 4.38: 2338 4.38 - 4.90: 4104 Nonbonded interactions: 10428 Sorted by model distance: nonbonded pdb=" O LYS A 128 " pdb=" OG1 THR A 129 " model vdw 2.325 3.040 nonbonded pdb=" O SER A 35 " pdb=" O THR A 58 " model vdw 2.496 3.040 nonbonded pdb=" O SER A 103 " pdb=" OG SER A 104 " model vdw 2.511 3.040 nonbonded pdb=" OG SER A 60 " pdb=" OG1 THR A 65 " model vdw 2.519 3.040 nonbonded pdb=" OD2 ASP A 30 " pdb=" NH1 ARG A 64 " model vdw 2.539 3.120 ... (remaining 10423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.530 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 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 : 0.003 0.031 1365 Z= 0.191 Angle : 0.642 5.714 1840 Z= 0.390 Chirality : 0.038 0.133 209 Planarity : 0.009 0.066 222 Dihedral : 12.389 43.192 460 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: 0.22 (0.60), residues: 164 helix: 0.86 (0.44), residues: 109 sheet: -0.20 (1.97), residues: 10 loop : -1.40 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 177 HIS 0.004 0.002 HIS A 59 PHE 0.016 0.002 PHE A 96 TYR 0.016 0.004 TYR A 180 ARG 0.012 0.003 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.5076 time to fit residues: 17.3439 Evaluate side-chains 27 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.273307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.270144 restraints weight = 1229.395| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 0.25 r_work: 0.4655 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4613 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1365 Z= 0.254 Angle : 0.654 7.678 1840 Z= 0.345 Chirality : 0.045 0.160 209 Planarity : 0.004 0.033 222 Dihedral : 5.092 16.434 183 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.91 % Allowed : 8.63 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.71), residues: 164 helix: 2.44 (0.49), residues: 112 sheet: -0.24 (1.98), residues: 10 loop : -0.55 (1.14), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 177 HIS 0.003 0.002 HIS A 59 PHE 0.008 0.001 PHE A 115 TYR 0.013 0.003 TYR A 175 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.134 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 31 average time/residue: 0.5314 time to fit residues: 17.0377 Evaluate side-chains 25 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 overall best weight: 0.0934 ------------------------------------------------------------------------------- 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 = 0.4751 r_free = 0.4751 target = 0.278279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.275028 restraints weight = 1211.862| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 0.27 r_work: 0.4700 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4657 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1365 Z= 0.163 Angle : 0.535 7.091 1840 Z= 0.281 Chirality : 0.040 0.128 209 Planarity : 0.003 0.035 222 Dihedral : 4.506 15.944 183 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.76 % Allowed : 12.95 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.71), residues: 164 helix: 2.88 (0.50), residues: 114 sheet: -0.50 (1.80), residues: 10 loop : -1.40 (1.03), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 179 TYR 0.010 0.002 TYR A 34 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.122 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 38 average time/residue: 0.4730 time to fit residues: 18.5842 Evaluate side-chains 29 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.0670 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.3980 chunk 7 optimal weight: 0.0980 chunk 14 optimal weight: 0.0870 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.278550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.275347 restraints weight = 1197.803| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 0.27 r_work: 0.4702 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.4658 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1365 Z= 0.155 Angle : 0.501 6.149 1840 Z= 0.269 Chirality : 0.039 0.115 209 Planarity : 0.003 0.033 222 Dihedral : 4.347 16.188 183 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.47 % Allowed : 15.11 % Favored : 78.42 % 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: 2.59 (0.71), residues: 164 helix: 2.95 (0.49), residues: 114 sheet: -0.61 (1.71), residues: 10 loop : -1.51 (1.05), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 179 TYR 0.010 0.001 TYR A 175 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.143 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.4921 time to fit residues: 18.3439 Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.0970 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.0670 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 overall best weight: 0.1116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.277396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.274318 restraints weight = 1187.397| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 0.27 r_work: 0.4694 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.4650 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1365 Z= 0.180 Angle : 0.555 8.686 1840 Z= 0.283 Chirality : 0.040 0.115 209 Planarity : 0.003 0.033 222 Dihedral : 4.375 15.442 183 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 7.19 % Allowed : 14.39 % Favored : 78.42 % 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: 2.57 (0.70), residues: 164 helix: 2.97 (0.49), residues: 114 sheet: -0.58 (1.71), residues: 10 loop : -1.65 (1.01), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.013 0.002 TYR A 34 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.139 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 36 average time/residue: 0.4930 time to fit residues: 18.3952 Evaluate side-chains 30 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 overall best weight: 0.0934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.277943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.274709 restraints weight = 1182.104| |-----------------------------------------------------------------------------| r_work (start): 0.4726 rms_B_bonded: 0.27 r_work: 0.4698 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4653 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1365 Z= 0.156 Angle : 0.505 6.885 1840 Z= 0.268 Chirality : 0.039 0.115 209 Planarity : 0.003 0.032 222 Dihedral : 4.249 15.473 183 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.91 % Allowed : 15.83 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.70), residues: 164 helix: 3.09 (0.49), residues: 114 sheet: -0.58 (1.66), residues: 10 loop : -1.81 (1.01), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.009 0.001 TYR A 175 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: A 40 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5871 (tmtt) REVERT: A 94 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4699 (mp0) outliers start: 11 outliers final: 5 residues processed: 35 average time/residue: 0.5138 time to fit residues: 18.6275 Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 0.2980 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.274824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.271328 restraints weight = 1226.328| |-----------------------------------------------------------------------------| r_work (start): 0.4695 rms_B_bonded: 0.28 r_work: 0.4666 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4621 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1365 Z= 0.227 Angle : 0.604 8.630 1840 Z= 0.305 Chirality : 0.041 0.130 209 Planarity : 0.003 0.032 222 Dihedral : 4.539 14.798 183 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.76 % Allowed : 17.27 % Favored : 76.98 % 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: 2.37 (0.69), residues: 164 helix: 2.93 (0.49), residues: 114 sheet: -0.69 (1.64), residues: 10 loop : -2.09 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 177 HIS 0.002 0.001 HIS A 204 PHE 0.006 0.001 PHE A 115 TYR 0.015 0.002 TYR A 34 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.127 Fit side-chains REVERT: A 40 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.5803 (tmtt) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.5279 time to fit residues: 18.0172 Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.0770 chunk 16 optimal weight: 0.1980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.272511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.269142 restraints weight = 1176.713| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 0.27 r_work: 0.4650 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4604 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1365 Z= 0.266 Angle : 0.628 7.198 1840 Z= 0.326 Chirality : 0.042 0.144 209 Planarity : 0.003 0.033 222 Dihedral : 4.707 15.634 183 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.47 % Allowed : 17.27 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.67), residues: 164 helix: 2.81 (0.48), residues: 113 sheet: -0.57 (1.67), residues: 10 loop : -2.13 (0.88), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 177 HIS 0.003 0.001 HIS A 204 PHE 0.007 0.001 PHE A 179 TYR 0.014 0.002 TYR A 175 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.125 Fit side-chains REVERT: A 40 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.5887 (tmtt) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.5851 time to fit residues: 18.7162 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 8 optimal weight: 0.1980 chunk 15 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.0870 chunk 12 optimal weight: 0.0970 overall best weight: 0.0870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.277707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.274526 restraints weight = 1188.308| |-----------------------------------------------------------------------------| r_work (start): 0.4717 rms_B_bonded: 0.26 r_work: 0.4694 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.4652 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1365 Z= 0.157 Angle : 0.524 7.132 1840 Z= 0.276 Chirality : 0.039 0.115 209 Planarity : 0.003 0.032 222 Dihedral : 4.251 14.973 183 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 5.04 % Allowed : 18.71 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.68), residues: 164 helix: 3.07 (0.48), residues: 114 sheet: -0.72 (1.58), residues: 10 loop : -2.08 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 179 TYR 0.009 0.001 TYR A 175 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.152 Fit side-chains REVERT: A 40 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.5680 (tmtt) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.4624 time to fit residues: 15.3934 Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 9 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.272828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.269554 restraints weight = 1167.987| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 0.26 r_work: 0.4651 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.4603 rms_B_bonded: 1.63 restraints_weight: 0.2500 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1365 Z= 0.299 Angle : 0.699 8.815 1840 Z= 0.348 Chirality : 0.044 0.149 209 Planarity : 0.004 0.033 222 Dihedral : 4.727 15.957 183 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.60 % Allowed : 20.86 % Favored : 75.54 % 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: 2.14 (0.68), residues: 164 helix: 2.74 (0.48), residues: 114 sheet: -0.54 (1.65), residues: 10 loop : -2.22 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 177 HIS 0.003 0.001 HIS A 204 PHE 0.008 0.002 PHE A 179 TYR 0.016 0.003 TYR A 175 ARG 0.004 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.136 Fit side-chains REVERT: A 40 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.5922 (tmtt) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.5272 time to fit residues: 16.4339 Evaluate side-chains 30 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 16 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.0956 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.277438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.274178 restraints weight = 1214.316| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 0.27 r_work: 0.4694 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.4648 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1365 Z= 0.178 Angle : 0.589 8.507 1840 Z= 0.295 Chirality : 0.040 0.115 209 Planarity : 0.003 0.032 222 Dihedral : 4.323 15.159 183 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.60 % Allowed : 21.58 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.69), residues: 164 helix: 3.05 (0.48), residues: 114 sheet: -0.57 (1.64), residues: 10 loop : -2.05 (0.95), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.002 0.000 HIS A 59 PHE 0.008 0.001 PHE A 179 TYR 0.011 0.002 TYR A 175 ARG 0.001 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.03 seconds wall clock time: 30 minutes 17.54 seconds (1817.54 seconds total)