Starting phenix.real_space_refine on Wed Mar 5 14:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023.map" model { file = "/net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v85_43023/03_2025/8v85_43023_neut.cif" } resolution = 2.9 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= 0.001 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 8 5.16 5 C 986 2.51 5 N 268 2.21 5 O 277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1539 Number of models: 1 Model: "" Number of chains: 1 Chain: "3" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1539 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Time building chain proxies: 2.08, per 1000 atoms: 1.35 Number of scatterers: 1539 At special positions: 0 Unit cell: (59.4, 59.4, 52.92, 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 8 16.00 O 277 8.00 N 268 7.00 C 986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 174.3 milliseconds 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 368 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 57.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain '3' and resid 146 through 155 Processing helix chain '3' and resid 161 through 173 Proline residue: 3 169 - end of helix Processing helix chain '3' and resid 188 through 199 Proline residue: 3 194 - end of helix Processing helix chain '3' and resid 216 through 232 Processing helix chain '3' and resid 246 through 256 Processing helix chain '3' and resid 264 through 276 Processing helix chain '3' and resid 278 through 282 removed outlier: 4.164A pdb=" N SER 3 281 " --> pdb=" O ASP 3 278 " (cutoff:3.500A) Processing helix chain '3' and resid 289 through 297 Processing helix chain '3' and resid 298 through 309 removed outlier: 3.548A pdb=" N GLU 3 304 " --> pdb=" O GLU 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain '3' and resid 238 through 241 removed outlier: 6.138A pdb=" N VAL 3 239 " --> pdb=" O ILE 3 262 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA 3 210 " --> pdb=" O ILE 3 261 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA 3 263 " --> pdb=" O ALA 3 210 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE 3 212 " --> pdb=" O ALA 3 263 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL 3 211 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP 3 288 " --> pdb=" O VAL 3 211 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU 3 213 " --> pdb=" O ASP 3 288 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL 3 285 " --> pdb=" O LEU 3 316 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE 3 318 " --> pdb=" O VAL 3 285 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE 3 287 " --> pdb=" O PHE 3 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 3 177 " --> pdb=" O THR 3 315 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 210 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: 0.42 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: 506 1.34 - 1.46: 262 1.46 - 1.57: 779 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 1563 Sorted by residual: bond pdb=" CA THR 3 312 " pdb=" CB THR 3 312 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.32e-02 5.74e+03 3.59e-01 bond pdb=" CA THR 3 312 " pdb=" C THR 3 312 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.10e-02 8.26e+03 2.91e-01 bond pdb=" C LYS 3 198 " pdb=" N LEU 3 199 " ideal model delta sigma weight residual 1.331 1.338 -0.007 1.25e-02 6.40e+03 2.85e-01 bond pdb=" CA ILE 3 168 " pdb=" C ILE 3 168 " ideal model delta sigma weight residual 1.520 1.524 -0.004 8.80e-03 1.29e+04 2.21e-01 bond pdb=" CA LEU 3 193 " pdb=" C LEU 3 193 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.01e-01 ... (remaining 1558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 2065 1.33 - 2.66: 27 2.66 - 3.98: 13 3.98 - 5.31: 2 5.31 - 6.64: 1 Bond angle restraints: 2108 Sorted by residual: angle pdb=" C ALA 3 263 " pdb=" N THR 3 264 " pdb=" CA THR 3 264 " ideal model delta sigma weight residual 120.94 127.58 -6.64 1.90e+00 2.77e-01 1.22e+01 angle pdb=" N GLY 3 244 " pdb=" CA GLY 3 244 " pdb=" C GLY 3 244 " ideal model delta sigma weight residual 115.08 112.16 2.92 1.19e+00 7.06e-01 6.04e+00 angle pdb=" CA PHE 3 298 " pdb=" C PHE 3 298 " pdb=" O PHE 3 298 " ideal model delta sigma weight residual 119.23 116.51 2.72 1.54e+00 4.22e-01 3.11e+00 angle pdb=" CA THR 3 312 " pdb=" C THR 3 312 " pdb=" N ARG 3 313 " ideal model delta sigma weight residual 114.76 116.67 -1.91 1.14e+00 7.69e-01 2.80e+00 angle pdb=" CA THR 3 312 " pdb=" C THR 3 312 " pdb=" O THR 3 312 " ideal model delta sigma weight residual 122.64 120.61 2.03 1.25e+00 6.40e-01 2.64e+00 ... (remaining 2103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.18: 847 9.18 - 18.35: 91 18.35 - 27.53: 18 27.53 - 36.71: 6 36.71 - 45.88: 6 Dihedral angle restraints: 968 sinusoidal: 403 harmonic: 565 Sorted by residual: dihedral pdb=" N LYS 3 155 " pdb=" CA LYS 3 155 " pdb=" CB LYS 3 155 " pdb=" CG LYS 3 155 " ideal model delta sinusoidal sigma weight residual -180.00 -134.12 -45.88 3 1.50e+01 4.44e-03 8.24e+00 dihedral pdb=" N LYS 3 228 " pdb=" CA LYS 3 228 " pdb=" CB LYS 3 228 " pdb=" CG LYS 3 228 " ideal model delta sinusoidal sigma weight residual -60.00 -103.18 43.18 3 1.50e+01 4.44e-03 7.76e+00 dihedral pdb=" CA ALA 3 263 " pdb=" C ALA 3 263 " pdb=" N THR 3 264 " pdb=" CA THR 3 264 " ideal model delta harmonic sigma weight residual 180.00 166.40 13.60 0 5.00e+00 4.00e-02 7.39e+00 ... (remaining 965 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 162 0.027 - 0.054: 49 0.054 - 0.081: 19 0.081 - 0.107: 13 0.107 - 0.134: 8 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE 3 261 " pdb=" N ILE 3 261 " pdb=" C ILE 3 261 " pdb=" CB ILE 3 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE 3 212 " pdb=" N ILE 3 212 " pdb=" C ILE 3 212 " pdb=" CB ILE 3 212 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL 3 178 " pdb=" N VAL 3 178 " pdb=" C VAL 3 178 " pdb=" CB VAL 3 178 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 248 not shown) Planarity restraints: 269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR 3 161 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO 3 162 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO 3 162 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO 3 162 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 168 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO 3 169 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO 3 169 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 3 169 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 191 " 0.006 2.00e-02 2.50e+03 5.13e-03 4.61e-01 pdb=" CG PHE 3 191 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 191 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 191 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 191 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 3 191 " 0.001 2.00e-02 2.50e+03 ... (remaining 266 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 499 2.85 - 3.37: 1485 3.37 - 3.88: 2523 3.88 - 4.39: 2831 4.39 - 4.90: 4700 Nonbonded interactions: 12038 Sorted by model distance: nonbonded pdb=" O ASP 3 245 " pdb=" NH2 ARG 3 267 " model vdw 2.342 3.120 nonbonded pdb=" NH2 ARG 3 209 " pdb=" OD2 ASP 3 259 " model vdw 2.364 3.120 nonbonded pdb=" OE1 GLN 3 250 " pdb=" NE ARG 3 267 " model vdw 2.407 3.120 nonbonded pdb=" N GLN 3 301 " pdb=" OE1 GLN 3 301 " model vdw 2.439 3.120 nonbonded pdb=" O ILE 3 163 " pdb=" OG1 THR 3 167 " model vdw 2.486 3.040 ... (remaining 12033 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: 2.550 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: 9.480 Find NCS groups from input model: 0.020 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1563 Z= 0.119 Angle : 0.504 6.641 2108 Z= 0.280 Chirality : 0.041 0.134 251 Planarity : 0.003 0.025 269 Dihedral : 8.921 45.882 600 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.61), residues: 195 helix: 1.64 (0.52), residues: 108 sheet: 0.27 (0.76), residues: 39 loop : -0.15 (0.89), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS 3 270 PHE 0.012 0.001 PHE 3 191 TYR 0.006 0.001 TYR 3 284 ARG 0.002 0.000 ARG 3 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.5775 time to fit residues: 36.8915 Evaluate side-chains 14 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 150 ASN 3 159 GLN 3 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.119387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.105814 restraints weight = 247218.536| |-----------------------------------------------------------------------------| r_work (start): 0.4830 rms_B_bonded: 59.19 r_work: 0.4407 rms_B_bonded: 43.62 restraints_weight: 2.0000 r_work: 0.4531 rms_B_bonded: 31.39 restraints_weight: 4.0000 r_work: 0.4935 rms_B_bonded: 12.87 restraints_weight: 8.0000 r_work (final): 0.4935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3495 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1563 Z= 0.219 Angle : 0.603 4.809 2108 Z= 0.306 Chirality : 0.044 0.161 251 Planarity : 0.004 0.028 269 Dihedral : 4.235 13.715 210 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.33 % Allowed : 7.56 % Favored : 90.12 % 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: 0.69 (0.60), residues: 195 helix: 0.99 (0.50), residues: 107 sheet: 0.06 (0.85), residues: 38 loop : -0.08 (0.87), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS 3 202 PHE 0.010 0.002 PHE 3 268 TYR 0.004 0.002 TYR 3 284 ARG 0.007 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.200 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 1.1629 time to fit residues: 20.3123 Evaluate side-chains 16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4941 r_free = 0.4941 target = 0.116674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.101255 restraints weight = 245649.728| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 73.49 r_work: 0.4335 rms_B_bonded: 51.32 restraints_weight: 2.0000 r_work: 0.4486 rms_B_bonded: 37.93 restraints_weight: 4.0000 r_work: 0.4871 rms_B_bonded: 16.74 restraints_weight: 8.0000 r_work (final): 0.4871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3213 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1563 Z= 0.180 Angle : 0.562 6.923 2108 Z= 0.275 Chirality : 0.042 0.145 251 Planarity : 0.005 0.037 269 Dihedral : 4.215 15.588 210 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 10.47 % Favored : 86.63 % 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: 0.42 (0.61), residues: 195 helix: 0.94 (0.52), residues: 107 sheet: -0.40 (0.98), residues: 28 loop : -0.39 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS 3 202 PHE 0.008 0.001 PHE 3 294 TYR 0.002 0.001 TYR 3 284 ARG 0.005 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: 3 146 LYS cc_start: 0.9446 (tppt) cc_final: 0.9154 (tppt) REVERT: 3 191 PHE cc_start: -0.3396 (p90) cc_final: -0.3655 (p90) REVERT: 3 221 MET cc_start: 0.1703 (mmt) cc_final: 0.1004 (tmm) outliers start: 5 outliers final: 1 residues processed: 19 average time/residue: 1.2509 time to fit residues: 24.3099 Evaluate side-chains 15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.5020 r_free = 0.5020 target = 0.119568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.106581 restraints weight = 16719.319| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 12.37 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3205 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 1563 Z= 0.323 Angle : 0.804 10.827 2108 Z= 0.394 Chirality : 0.045 0.151 251 Planarity : 0.007 0.072 269 Dihedral : 5.377 17.783 210 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 11.05 % Favored : 87.21 % 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: -0.02 (0.64), residues: 195 helix: 0.39 (0.53), residues: 105 sheet: -0.89 (0.90), residues: 39 loop : 0.32 (0.95), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS 3 270 PHE 0.015 0.002 PHE 3 230 TYR 0.008 0.004 TYR 3 284 ARG 0.006 0.001 ARG 3 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.172 Fit side-chains REVERT: 3 221 MET cc_start: 0.1585 (mmt) cc_final: 0.1152 (tmm) REVERT: 3 275 MET cc_start: 0.4991 (ptt) cc_final: 0.4303 (pmm) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 1.3270 time to fit residues: 25.7340 Evaluate side-chains 15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 191 PHE Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4846 r_free = 0.4846 target = 0.113735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.104226 restraints weight = 22016.332| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 11.26 r_work (final): 0.4815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2850 moved from start: 0.8244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1563 Z= 0.232 Angle : 0.730 14.463 2108 Z= 0.345 Chirality : 0.043 0.132 251 Planarity : 0.005 0.034 269 Dihedral : 5.239 17.774 210 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.16 % Allowed : 13.95 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.63), residues: 195 helix: 0.41 (0.54), residues: 105 sheet: -1.08 (1.08), residues: 26 loop : -0.57 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.007 0.001 PHE 3 230 TYR 0.011 0.003 TYR 3 284 ARG 0.004 0.001 ARG 3 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.194 Fit side-chains REVERT: 3 195 MET cc_start: -0.0050 (mmt) cc_final: -0.0748 (tpt) REVERT: 3 275 MET cc_start: 0.4825 (ptt) cc_final: 0.4316 (pmm) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 1.2258 time to fit residues: 22.6424 Evaluate side-chains 16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.4947 r_free = 0.4947 target = 0.114924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.104004 restraints weight = 16850.296| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 9.23 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2577 moved from start: 0.8890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1563 Z= 0.240 Angle : 0.750 12.717 2108 Z= 0.353 Chirality : 0.044 0.125 251 Planarity : 0.005 0.034 269 Dihedral : 5.094 17.062 210 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.58 % Allowed : 15.70 % Favored : 83.72 % 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: -0.24 (0.64), residues: 195 helix: 0.51 (0.55), residues: 103 sheet: -1.75 (0.92), residues: 34 loop : -0.01 (0.85), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 3 202 PHE 0.006 0.001 PHE 3 268 TYR 0.010 0.003 TYR 3 284 ARG 0.004 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: 3 221 MET cc_start: 0.5492 (tmm) cc_final: 0.5289 (tmm) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 1.1471 time to fit residues: 20.0206 Evaluate side-chains 15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 151 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 = 0.4853 r_free = 0.4853 target = 0.108797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.098623 restraints weight = 17903.796| |-----------------------------------------------------------------------------| r_work (start): 0.4657 rms_B_bonded: 9.54 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3004 moved from start: 1.0473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 1563 Z= 0.293 Angle : 0.841 14.374 2108 Z= 0.401 Chirality : 0.047 0.133 251 Planarity : 0.006 0.053 269 Dihedral : 5.592 19.177 210 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.74 % Allowed : 16.28 % Favored : 81.98 % 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: -0.84 (0.62), residues: 195 helix: -0.02 (0.53), residues: 103 sheet: -1.30 (1.26), residues: 15 loop : -0.98 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 202 PHE 0.008 0.002 PHE 3 268 TYR 0.013 0.004 TYR 3 284 ARG 0.004 0.001 ARG 3 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.170 Fit side-chains REVERT: 3 275 MET cc_start: 0.4363 (ptt) cc_final: 0.4018 (ptt) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 1.3441 time to fit residues: 22.0564 Evaluate side-chains 16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 195 MET Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4859 r_free = 0.4859 target = 0.107647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.096906 restraints weight = 18218.887| |-----------------------------------------------------------------------------| r_work (start): 0.4697 rms_B_bonded: 9.99 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2588 moved from start: 1.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1563 Z= 0.264 Angle : 0.808 12.280 2108 Z= 0.386 Chirality : 0.046 0.141 251 Planarity : 0.005 0.038 269 Dihedral : 5.265 17.401 210 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.33 % Allowed : 17.44 % Favored : 80.23 % 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: -0.97 (0.62), residues: 195 helix: 0.06 (0.53), residues: 103 sheet: -2.39 (0.85), residues: 34 loop : -0.40 (0.85), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 3 202 PHE 0.011 0.002 PHE 3 191 TYR 0.009 0.003 TYR 3 284 ARG 0.003 0.001 ARG 3 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.172 Fit side-chains REVERT: 3 195 MET cc_start: 0.1324 (OUTLIER) cc_final: 0.0888 (tpt) REVERT: 3 253 MET cc_start: -0.1831 (tpt) cc_final: -0.2058 (ppp) outliers start: 4 outliers final: 1 residues processed: 16 average time/residue: 1.0889 time to fit residues: 17.9476 Evaluate side-chains 16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 195 MET Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.0040 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.107764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.099732 restraints weight = 21490.810| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 9.68 r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2689 moved from start: 1.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1563 Z= 0.211 Angle : 0.791 14.449 2108 Z= 0.365 Chirality : 0.045 0.161 251 Planarity : 0.004 0.034 269 Dihedral : 4.902 15.665 210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.74 % Allowed : 18.60 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.61), residues: 195 helix: 0.14 (0.54), residues: 104 sheet: -2.40 (0.84), residues: 34 loop : -0.88 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.013 0.002 PHE 3 230 TYR 0.008 0.003 TYR 3 284 ARG 0.002 0.000 ARG 3 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.172 Fit side-chains REVERT: 3 195 MET cc_start: 0.1109 (mmt) cc_final: 0.0771 (tpt) REVERT: 3 275 MET cc_start: 0.4663 (ptt) cc_final: 0.4145 (pmm) outliers start: 3 outliers final: 1 residues processed: 16 average time/residue: 1.1238 time to fit residues: 18.4822 Evaluate side-chains 14 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4912 r_free = 0.4912 target = 0.109427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.097739 restraints weight = 17532.983| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 10.86 r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2879 moved from start: 1.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1563 Z= 0.200 Angle : 0.821 14.158 2108 Z= 0.378 Chirality : 0.044 0.130 251 Planarity : 0.004 0.031 269 Dihedral : 4.688 14.757 210 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.58 % Allowed : 20.35 % Favored : 79.07 % 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: -0.89 (0.62), residues: 195 helix: 0.26 (0.54), residues: 104 sheet: -2.43 (0.84), residues: 34 loop : -0.63 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.017 0.002 PHE 3 230 TYR 0.006 0.002 TYR 3 284 ARG 0.002 0.000 ARG 3 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: 3 195 MET cc_start: 0.0539 (mmt) cc_final: 0.0268 (tpt) REVERT: 3 253 MET cc_start: -0.0413 (tpt) cc_final: -0.0980 (tpt) REVERT: 3 255 MET cc_start: 0.7363 (mtt) cc_final: 0.6123 (ttp) REVERT: 3 275 MET cc_start: 0.5228 (ptt) cc_final: 0.4656 (pmm) outliers start: 1 outliers final: 2 residues processed: 14 average time/residue: 1.0549 time to fit residues: 15.2531 Evaluate side-chains 15 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 50.0000 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.4896 r_free = 0.4896 target = 0.106673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.095656 restraints weight = 18001.897| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 10.28 r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2833 moved from start: 1.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1563 Z= 0.223 Angle : 0.842 15.111 2108 Z= 0.387 Chirality : 0.044 0.131 251 Planarity : 0.004 0.029 269 Dihedral : 4.789 15.276 210 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.58 % Allowed : 20.35 % Favored : 79.07 % 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: -0.98 (0.62), residues: 195 helix: 0.20 (0.54), residues: 104 sheet: -2.45 (0.84), residues: 34 loop : -0.70 (0.81), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.012 0.002 PHE 3 230 TYR 0.007 0.002 TYR 3 284 ARG 0.003 0.001 ARG 3 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.12 seconds wall clock time: 44 minutes 44.29 seconds (2684.29 seconds total)