Starting phenix.real_space_refine on Sat Apr 26 14:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhv_43242/04_2025/8vhv_43242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhv_43242/04_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_43242/04_2025/8vhv_43242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhv_43242/04_2025/8vhv_43242.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhv_43242/04_2025/8vhv_43242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhv_43242/04_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 2.27, per 1000 atoms: 1.70 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: 0.31 Conformation dependent library (CDL) restraints added in 148.4 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: 0.34 Time building geometry restraints manager: 0.39 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.100 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: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- 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 1367 Z= 0.164 Angle : 0.642 5.714 1844 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 Details of bonding type rmsd hydrogen bonds : bond 0.14511 ( 104) hydrogen bonds : angle 5.57714 ( 303) SS BOND : bond 0.00543 ( 2) SS BOND : angle 0.72632 ( 4) covalent geometry : bond 0.00305 ( 1365) covalent geometry : angle 0.64159 ( 1840) *********************** 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 : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.5020 time to fit residues: 17.1308 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 1367 Z= 0.182 Angle : 0.653 7.678 1844 Z= 0.344 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 Details of bonding type rmsd hydrogen bonds : bond 0.05360 ( 104) hydrogen bonds : angle 4.07459 ( 303) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.23782 ( 4) covalent geometry : bond 0.00390 ( 1365) covalent geometry : angle 0.65395 ( 1840) *********************** 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 : 0.135 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 31 average time/residue: 0.5182 time to fit residues: 16.6223 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 : 0.133 ------------------------------------------------------------------------------- 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 1367 Z= 0.125 Angle : 0.535 7.091 1844 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 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 104) hydrogen bonds : angle 3.74429 ( 303) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.45903 ( 4) covalent geometry : bond 0.00255 ( 1365) covalent geometry : angle 0.53479 ( 1840) *********************** 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 : 0.133 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 38 average time/residue: 0.5127 time to fit residues: 20.1376 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 : 0.137 ------------------------------------------------------------------------------- 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 1367 Z= 0.118 Angle : 0.501 6.149 1844 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 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 104) hydrogen bonds : angle 3.60501 ( 303) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.49173 ( 4) covalent geometry : bond 0.00243 ( 1365) covalent geometry : angle 0.50097 ( 1840) *********************** 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 : 0.136 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.4593 time to fit residues: 17.1312 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.0670 chunk 10 optimal weight: 0.0670 chunk 8 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 overall best weight: 0.0854 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.278498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.275369 restraints weight = 1194.879| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 0.27 r_work: 0.4704 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4659 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1367 Z= 0.119 Angle : 0.536 8.767 1844 Z= 0.274 Chirality : 0.039 0.116 209 Planarity : 0.003 0.033 222 Dihedral : 4.272 15.686 183 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.24 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: 2.66 (0.70), residues: 164 helix: 3.03 (0.49), residues: 114 sheet: -0.61 (1.71), residues: 10 loop : -1.60 (1.02), 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 0.011 0.002 TYR A 34 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 104) hydrogen bonds : angle 3.56766 ( 303) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.57660 ( 4) covalent geometry : bond 0.00244 ( 1365) covalent geometry : angle 0.53624 ( 1840) *********************** 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: 9 poor density : 30 time to evaluate : 0.136 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 0.4725 time to fit residues: 18.1226 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 15 optimal weight: 0.3980 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 overall best weight: 0.1176 ------------------------------------------------------------------------------- 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 = 0.4740 r_free = 0.4740 target = 0.276976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.273655 restraints weight = 1179.881| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 0.27 r_work: 0.4686 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4641 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1367 Z= 0.129 Angle : 0.533 6.996 1844 Z= 0.278 Chirality : 0.039 0.116 209 Planarity : 0.003 0.033 222 Dihedral : 4.323 15.014 183 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.76 % Allowed : 18.71 % 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: 2.57 (0.70), residues: 164 helix: 3.03 (0.49), residues: 114 sheet: -0.63 (1.66), residues: 10 loop : -1.86 (1.00), 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 0.009 0.002 TYR A 175 ARG 0.000 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 104) hydrogen bonds : angle 3.63659 ( 303) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.50652 ( 4) covalent geometry : bond 0.00272 ( 1365) covalent geometry : angle 0.53306 ( 1840) *********************** 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 35 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.142 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.4918 time to fit residues: 16.3360 Evaluate side-chains 31 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.0770 chunk 6 optimal weight: 0.0570 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 0.0870 overall best weight: 0.0810 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.278732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.275372 restraints weight = 1239.781| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 0.29 r_work: 0.4704 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4660 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1367 Z= 0.117 Angle : 0.550 8.674 1844 Z= 0.275 Chirality : 0.039 0.116 209 Planarity : 0.003 0.032 222 Dihedral : 4.195 15.277 183 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.76 % Allowed : 18.71 % 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: 2.67 (0.70), residues: 164 helix: 3.12 (0.48), residues: 114 sheet: -0.73 (1.60), residues: 10 loop : -1.83 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.010 0.001 TYR A 34 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 104) hydrogen bonds : angle 3.57589 ( 303) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.54294 ( 4) covalent geometry : bond 0.00243 ( 1365) covalent geometry : angle 0.54959 ( 1840) *********************** 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 : 0.140 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.5547 time to fit residues: 18.9097 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.0980 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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 = 0.4732 r_free = 0.4732 target = 0.275644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.272218 restraints weight = 1183.275| |-----------------------------------------------------------------------------| r_work (start): 0.4705 rms_B_bonded: 0.27 r_work: 0.4674 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4630 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1367 Z= 0.147 Angle : 0.569 7.882 1844 Z= 0.294 Chirality : 0.040 0.128 209 Planarity : 0.003 0.032 222 Dihedral : 4.455 14.848 183 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.76 % Allowed : 17.99 % 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: 2.40 (0.69), residues: 164 helix: 2.97 (0.48), residues: 114 sheet: -0.66 (1.62), residues: 10 loop : -2.19 (0.90), 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 0.010 0.002 TYR A 34 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 104) hydrogen bonds : angle 3.73751 ( 303) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.50542 ( 4) covalent geometry : bond 0.00316 ( 1365) covalent geometry : angle 0.56873 ( 1840) *********************** 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: 8 poor density : 27 time to evaluate : 0.128 Fit side-chains REVERT: A 40 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6105 (tmtt) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.5374 time to fit residues: 18.3327 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 : 0.156 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 7 optimal weight: 0.0030 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 chunk 8 optimal weight: 0.0970 chunk 15 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 overall best weight: 0.0746 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.278732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.275525 restraints weight = 1174.673| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 0.26 r_work: 0.4702 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4659 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1367 Z= 0.113 Angle : 0.520 8.285 1844 Z= 0.269 Chirality : 0.038 0.115 209 Planarity : 0.003 0.032 222 Dihedral : 4.176 15.766 183 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 5.76 % Allowed : 17.99 % 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: 2.64 (0.69), residues: 164 helix: 3.17 (0.48), residues: 114 sheet: -0.78 (1.56), residues: 10 loop : -2.08 (0.94), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.002 0.000 HIS A 59 PHE 0.007 0.001 PHE A 179 TYR 0.008 0.001 TYR A 175 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 104) hydrogen bonds : angle 3.58031 ( 303) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.50085 ( 4) covalent geometry : bond 0.00231 ( 1365) covalent geometry : angle 0.51981 ( 1840) *********************** 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 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: A 40 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5967 (tmtt) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.4661 time to fit residues: 16.4828 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 195 LEU 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: 0.0870 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 overall best weight: 0.1336 ------------------------------------------------------------------------------- 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 = 0.4738 r_free = 0.4738 target = 0.276496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.273130 restraints weight = 1188.908| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 0.26 r_work: 0.4684 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.4642 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1367 Z= 0.137 Angle : 0.561 7.933 1844 Z= 0.289 Chirality : 0.039 0.122 209 Planarity : 0.003 0.032 222 Dihedral : 4.332 15.015 183 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.60 % Allowed : 20.14 % 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: 2.49 (0.69), residues: 164 helix: 3.06 (0.48), residues: 114 sheet: -0.58 (1.62), residues: 10 loop : -2.22 (0.95), 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 115 TYR 0.011 0.002 TYR A 34 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 104) hydrogen bonds : angle 3.67503 ( 303) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.49172 ( 4) covalent geometry : bond 0.00293 ( 1365) covalent geometry : angle 0.56118 ( 1840) ********************** 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 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.139 Fit side-chains REVERT: A 23 MET cc_start: 0.6757 (tpt) cc_final: 0.6496 (tpt) REVERT: A 40 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6060 (tmtt) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.4716 time to fit residues: 15.6993 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 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 58 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 16 optimal weight: 0.0470 chunk 11 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 0.0870 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 overall best weight: 0.1656 ------------------------------------------------------------------------------- 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 = 0.4731 r_free = 0.4731 target = 0.275411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.272031 restraints weight = 1188.539| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 0.26 r_work: 0.4670 rms_B_bonded: 0.69 restraints_weight: 0.5000 r_work: 0.4627 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1367 Z= 0.153 Angle : 0.586 7.918 1844 Z= 0.302 Chirality : 0.041 0.129 209 Planarity : 0.003 0.033 222 Dihedral : 4.488 14.766 183 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.32 % Allowed : 20.14 % 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: 2.37 (0.69), residues: 164 helix: 2.96 (0.48), residues: 114 sheet: -0.53 (1.66), residues: 10 loop : -2.26 (0.92), 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 59 PHE 0.006 0.001 PHE A 115 TYR 0.012 0.002 TYR A 34 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 104) hydrogen bonds : angle 3.79351 ( 303) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.42957 ( 4) covalent geometry : bond 0.00331 ( 1365) covalent geometry : angle 0.58634 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.42 seconds wall clock time: 31 minutes 45.15 seconds (1905.15 seconds total)