Starting phenix.real_space_refine on Wed Mar 5 14:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxy_38765/03_2025/8xxy_38765.cif" } resolution = 3.68 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= 1.000 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 14 5.16 5 C 1216 2.51 5 N 314 2.21 5 O 294 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: 1838 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1838 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 3 Time building chain proxies: 1.94, per 1000 atoms: 1.06 Number of scatterers: 1838 At special positions: 0 Unit cell: (58.1, 66.4, 73.6625, 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 14 16.00 O 294 8.00 N 314 7.00 C 1216 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: 0.48 Conformation dependent library (CDL) restraints added in 220.7 milliseconds 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 446 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 59 through 80 Processing helix chain 'R' and resid 86 through 110 removed outlier: 3.531A pdb=" N THR R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 127 through 154 Processing helix chain 'R' and resid 168 through 188 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 209 through 224 removed outlier: 4.010A pdb=" N PHE R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 244 Processing helix chain 'R' and resid 249 through 284 Proline residue: R 270 - end of helix removed outlier: 3.531A pdb=" N VAL R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 319 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 332 removed outlier: 3.588A pdb=" N ARG R 326 " --> pdb=" O GLY R 322 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 474 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: 0.51 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 569 1.35 - 1.46: 446 1.46 - 1.58: 839 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 1874 Sorted by residual: bond pdb=" N LEU R 59 " pdb=" CA LEU R 59 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" CA TYR R 271 " pdb=" CB TYR R 271 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.63e-02 3.76e+03 3.89e-01 bond pdb=" CA PRO R 270 " pdb=" C PRO R 270 " ideal model delta sigma weight residual 1.516 1.526 -0.010 1.61e-02 3.86e+03 3.61e-01 bond pdb=" CA TRP R 268 " pdb=" C TRP R 268 " ideal model delta sigma weight residual 1.519 1.526 -0.007 1.22e-02 6.72e+03 3.08e-01 bond pdb=" N GLY R 67 " pdb=" CA GLY R 67 " ideal model delta sigma weight residual 1.454 1.447 0.007 1.24e-02 6.50e+03 3.06e-01 ... (remaining 1869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2367 0.83 - 1.65: 157 1.65 - 2.48: 19 2.48 - 3.31: 5 3.31 - 4.14: 3 Bond angle restraints: 2551 Sorted by residual: angle pdb=" N VAL R 244 " pdb=" CA VAL R 244 " pdb=" C VAL R 244 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 angle pdb=" C VAL R 296 " pdb=" CA VAL R 296 " pdb=" CB VAL R 296 " ideal model delta sigma weight residual 112.22 109.83 2.39 1.38e+00 5.25e-01 2.99e+00 angle pdb=" C TRP R 176 " pdb=" N GLY R 177 " pdb=" CA GLY R 177 " ideal model delta sigma weight residual 120.00 121.83 -1.83 1.10e+00 8.26e-01 2.78e+00 angle pdb=" N VAL R 296 " pdb=" CA VAL R 296 " pdb=" C VAL R 296 " ideal model delta sigma weight residual 110.72 112.37 -1.65 1.01e+00 9.80e-01 2.66e+00 angle pdb=" C VAL R 298 " pdb=" CA VAL R 298 " pdb=" CB VAL R 298 " ideal model delta sigma weight residual 112.14 110.05 2.09 1.35e+00 5.49e-01 2.40e+00 ... (remaining 2546 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.94: 926 13.94 - 27.87: 114 27.87 - 41.80: 47 41.80 - 55.74: 7 55.74 - 69.67: 2 Dihedral angle restraints: 1096 sinusoidal: 408 harmonic: 688 Sorted by residual: dihedral pdb=" CA ARG R 255 " pdb=" CB ARG R 255 " pdb=" CG ARG R 255 " pdb=" CD ARG R 255 " ideal model delta sinusoidal sigma weight residual -180.00 -123.43 -56.57 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CG ARG R 246 " pdb=" CD ARG R 246 " pdb=" NE ARG R 246 " pdb=" CZ ARG R 246 " ideal model delta sinusoidal sigma weight residual -90.00 -130.31 40.31 2 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" N LYS R 324 " pdb=" CA LYS R 324 " pdb=" CB LYS R 324 " pdb=" CG LYS R 324 " ideal model delta sinusoidal sigma weight residual -180.00 -130.40 -49.60 3 1.50e+01 4.44e-03 8.80e+00 ... (remaining 1093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 215 0.022 - 0.044: 52 0.044 - 0.066: 27 0.066 - 0.087: 22 0.087 - 0.109: 5 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA PRO R 270 " pdb=" N PRO R 270 " pdb=" C PRO R 270 " pdb=" CB PRO R 270 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA ILE R 279 " pdb=" N ILE R 279 " pdb=" C ILE R 279 " pdb=" CB ILE R 279 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.42e-01 chirality pdb=" CA VAL R 244 " pdb=" N VAL R 244 " pdb=" C VAL R 244 " pdb=" CB VAL R 244 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.38e-01 ... (remaining 318 not shown) Planarity restraints: 303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 184 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO R 185 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 185 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 185 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 314 " -0.013 5.00e-02 4.00e+02 2.01e-02 6.46e-01 pdb=" N PRO R 315 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 226 " -0.013 5.00e-02 4.00e+02 1.95e-02 6.10e-01 pdb=" N PRO R 227 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 227 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 227 " -0.011 5.00e-02 4.00e+02 ... (remaining 300 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 545 2.83 - 3.35: 1951 3.35 - 3.87: 2946 3.87 - 4.38: 3240 4.38 - 4.90: 5438 Nonbonded interactions: 14120 Sorted by model distance: nonbonded pdb=" O ALA R 96 " pdb=" OG1 THR R 100 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN R 219 " pdb=" OH TYR R 271 " model vdw 2.352 3.040 nonbonded pdb=" O ALA R 265 " pdb=" OG1 THR R 269 " model vdw 2.374 3.040 nonbonded pdb=" O LEU R 242 " pdb=" OG SER R 245 " model vdw 2.392 3.040 nonbonded pdb=" O LEU R 102 " pdb=" OG1 THR R 105 " model vdw 2.407 3.040 ... (remaining 14115 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 0.034 1874 Z= 0.142 Angle : 0.474 4.137 2551 Z= 0.298 Chirality : 0.032 0.109 321 Planarity : 0.003 0.027 303 Dihedral : 14.533 69.667 650 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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: 2.29 (0.57), residues: 229 helix: 2.16 (0.38), residues: 198 sheet: None (None), residues: 0 loop : -3.01 (0.84), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.003 0.001 PHE R 147 TYR 0.004 0.001 TYR R 233 ARG 0.001 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.210 Fit side-chains REVERT: R 86 SER cc_start: 0.9025 (t) cc_final: 0.8294 (p) REVERT: R 132 ASN cc_start: 0.8277 (m-40) cc_final: 0.7996 (m110) REVERT: R 135 PHE cc_start: 0.8082 (t80) cc_final: 0.7122 (t80) REVERT: R 182 PHE cc_start: 0.7510 (t80) cc_final: 0.6636 (t80) REVERT: R 268 TRP cc_start: 0.7383 (m100) cc_final: 0.6709 (m100) REVERT: R 278 ASP cc_start: 0.8258 (t70) cc_final: 0.7897 (m-30) REVERT: R 311 CYS cc_start: 0.8217 (m) cc_final: 0.7978 (p) REVERT: R 313 LEU cc_start: 0.9019 (mt) cc_final: 0.8815 (mp) REVERT: R 318 TYR cc_start: 0.8664 (m-80) cc_final: 0.7903 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1620 time to fit residues: 13.9535 Evaluate side-chains 45 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 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 = 0.3889 r_free = 0.3889 target = 0.122200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099460 restraints weight = 4666.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101842 restraints weight = 2962.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103248 restraints weight = 2297.225| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1874 Z= 0.202 Angle : 0.645 8.556 2551 Z= 0.312 Chirality : 0.038 0.137 321 Planarity : 0.004 0.030 303 Dihedral : 3.513 14.318 259 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.13 % Allowed : 21.03 % Favored : 73.85 % 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: 2.51 (0.57), residues: 229 helix: 2.17 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -2.87 (1.05), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 268 HIS 0.004 0.002 HIS R 272 PHE 0.020 0.002 PHE R 131 TYR 0.013 0.002 TYR R 136 ARG 0.005 0.001 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.156 Fit side-chains REVERT: R 95 LEU cc_start: 0.9222 (tp) cc_final: 0.8999 (tt) REVERT: R 135 PHE cc_start: 0.8291 (t80) cc_final: 0.7601 (t80) REVERT: R 268 TRP cc_start: 0.7321 (m100) cc_final: 0.6727 (m100) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.0796 time to fit residues: 6.0853 Evaluate side-chains 43 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101790 restraints weight = 4901.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103986 restraints weight = 3135.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105255 restraints weight = 2441.919| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1874 Z= 0.170 Angle : 0.655 9.445 2551 Z= 0.305 Chirality : 0.037 0.133 321 Planarity : 0.004 0.025 303 Dihedral : 3.420 13.630 259 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.15 % Allowed : 23.08 % Favored : 70.77 % 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 (0.57), residues: 229 helix: 2.04 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.72 (1.17), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 268 HIS 0.005 0.001 HIS R 272 PHE 0.017 0.002 PHE R 131 TYR 0.008 0.001 TYR R 136 ARG 0.003 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: R 95 LEU cc_start: 0.9269 (tp) cc_final: 0.9066 (tt) REVERT: R 132 ASN cc_start: 0.7941 (m-40) cc_final: 0.7702 (m-40) REVERT: R 135 PHE cc_start: 0.8157 (t80) cc_final: 0.7454 (t80) REVERT: R 268 TRP cc_start: 0.7266 (m100) cc_final: 0.6635 (m100) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.0794 time to fit residues: 5.3251 Evaluate side-chains 44 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096704 restraints weight = 4840.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098925 restraints weight = 3107.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100249 restraints weight = 2428.768| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1874 Z= 0.307 Angle : 0.743 7.927 2551 Z= 0.348 Chirality : 0.041 0.141 321 Planarity : 0.004 0.023 303 Dihedral : 3.655 13.353 259 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.67 % Allowed : 23.08 % Favored : 70.26 % 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: 1.92 (0.56), residues: 229 helix: 1.71 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -2.28 (1.17), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 268 HIS 0.005 0.002 HIS R 237 PHE 0.014 0.002 PHE R 182 TYR 0.012 0.002 TYR R 136 ARG 0.003 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.8149 (m-40) cc_final: 0.7886 (m-40) REVERT: R 135 PHE cc_start: 0.8316 (t80) cc_final: 0.7560 (t80) REVERT: R 182 PHE cc_start: 0.7144 (t80) cc_final: 0.6937 (t80) REVERT: R 245 SER cc_start: 0.7873 (p) cc_final: 0.7308 (t) REVERT: R 254 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7184 (mtp) REVERT: R 268 TRP cc_start: 0.7360 (m100) cc_final: 0.6717 (m100) outliers start: 13 outliers final: 4 residues processed: 52 average time/residue: 0.0988 time to fit residues: 6.3563 Evaluate side-chains 48 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.121702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100066 restraints weight = 4874.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102466 restraints weight = 3059.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103924 restraints weight = 2344.192| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1874 Z= 0.179 Angle : 0.647 8.014 2551 Z= 0.301 Chirality : 0.036 0.129 321 Planarity : 0.004 0.026 303 Dihedral : 3.529 13.047 259 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.15 % Allowed : 22.05 % Favored : 71.79 % 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: 2.35 (0.57), residues: 229 helix: 1.95 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.75 (1.19), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.013 0.002 PHE R 131 TYR 0.011 0.001 TYR R 136 ARG 0.002 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8199 (t80) cc_final: 0.7677 (t80) REVERT: R 254 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: R 268 TRP cc_start: 0.7260 (m100) cc_final: 0.6597 (m100) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.1021 time to fit residues: 6.6675 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.121513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100806 restraints weight = 4774.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.103132 restraints weight = 3029.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104526 restraints weight = 2331.205| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1874 Z= 0.198 Angle : 0.750 10.213 2551 Z= 0.331 Chirality : 0.038 0.131 321 Planarity : 0.004 0.024 303 Dihedral : 3.508 12.340 259 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.10 % Allowed : 23.59 % Favored : 72.31 % 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 (0.57), residues: 229 helix: 2.04 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.64 (1.28), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.035 0.002 PHE R 182 TYR 0.010 0.001 TYR R 136 ARG 0.001 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.248 Fit side-chains REVERT: R 132 ASN cc_start: 0.7748 (m-40) cc_final: 0.7069 (t0) REVERT: R 135 PHE cc_start: 0.8210 (t80) cc_final: 0.7596 (t80) REVERT: R 136 TYR cc_start: 0.4490 (m-80) cc_final: 0.3975 (m-80) REVERT: R 254 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: R 268 TRP cc_start: 0.7349 (m100) cc_final: 0.6737 (m100) REVERT: R 318 TYR cc_start: 0.8797 (m-80) cc_final: 0.8548 (m-80) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0935 time to fit residues: 5.5635 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101565 restraints weight = 4819.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103893 restraints weight = 3003.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105164 restraints weight = 2306.407| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1874 Z= 0.177 Angle : 0.706 9.813 2551 Z= 0.312 Chirality : 0.037 0.130 321 Planarity : 0.003 0.025 303 Dihedral : 3.459 12.305 259 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 3.59 % Allowed : 24.10 % Favored : 72.31 % 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: 2.74 (0.58), residues: 229 helix: 2.21 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.60 (1.27), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.025 0.002 PHE R 182 TYR 0.010 0.001 TYR R 136 ARG 0.002 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.7780 (m-40) cc_final: 0.7072 (t0) REVERT: R 135 PHE cc_start: 0.8193 (t80) cc_final: 0.7610 (t80) REVERT: R 136 TYR cc_start: 0.4725 (m-80) cc_final: 0.4112 (m-80) REVERT: R 254 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: R 268 TRP cc_start: 0.7317 (m100) cc_final: 0.6646 (m100) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.0981 time to fit residues: 5.7599 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.100145 restraints weight = 4945.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102511 restraints weight = 3058.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103974 restraints weight = 2341.056| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1874 Z= 0.197 Angle : 0.752 14.108 2551 Z= 0.332 Chirality : 0.037 0.131 321 Planarity : 0.004 0.033 303 Dihedral : 3.442 11.622 259 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 5.13 % Allowed : 24.10 % Favored : 70.77 % 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: 2.79 (0.58), residues: 229 helix: 2.23 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.47 (1.31), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 PHE 0.026 0.002 PHE R 182 TYR 0.009 0.001 TYR R 136 ARG 0.001 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.7841 (m-40) cc_final: 0.7083 (t0) REVERT: R 135 PHE cc_start: 0.8224 (t80) cc_final: 0.7558 (t80) REVERT: R 136 TYR cc_start: 0.4707 (m-80) cc_final: 0.4251 (m-80) REVERT: R 254 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7194 (mpp) REVERT: R 268 TRP cc_start: 0.7337 (m100) cc_final: 0.6697 (m100) REVERT: R 318 TYR cc_start: 0.8762 (m-80) cc_final: 0.8552 (m-80) outliers start: 10 outliers final: 6 residues processed: 49 average time/residue: 0.1163 time to fit residues: 6.8235 Evaluate side-chains 45 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.0030 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.119834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098700 restraints weight = 4944.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100985 restraints weight = 3090.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102430 restraints weight = 2376.880| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1874 Z= 0.257 Angle : 0.780 12.150 2551 Z= 0.356 Chirality : 0.039 0.136 321 Planarity : 0.004 0.026 303 Dihedral : 3.587 13.606 259 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.10 % Allowed : 23.08 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.57), residues: 229 helix: 2.11 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.99 (1.16), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 330 HIS 0.004 0.001 HIS R 272 PHE 0.024 0.002 PHE R 182 TYR 0.009 0.002 TYR R 318 ARG 0.002 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.209 Fit side-chains REVERT: R 132 ASN cc_start: 0.7911 (m-40) cc_final: 0.7175 (t0) REVERT: R 135 PHE cc_start: 0.8263 (t80) cc_final: 0.7502 (t80) REVERT: R 136 TYR cc_start: 0.4834 (m-80) cc_final: 0.4435 (m-80) REVERT: R 254 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7115 (mtp) REVERT: R 268 TRP cc_start: 0.7293 (m100) cc_final: 0.6711 (m100) REVERT: R 318 TYR cc_start: 0.8716 (m-80) cc_final: 0.8491 (m-80) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.0988 time to fit residues: 5.8171 Evaluate side-chains 43 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.120991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100222 restraints weight = 4969.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102635 restraints weight = 3026.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104145 restraints weight = 2301.520| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1874 Z= 0.193 Angle : 0.759 11.824 2551 Z= 0.341 Chirality : 0.038 0.127 321 Planarity : 0.004 0.025 303 Dihedral : 3.585 12.204 259 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.59 % Allowed : 24.10 % Favored : 72.31 % 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: 2.72 (0.57), residues: 229 helix: 2.19 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.96 (1.11), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 330 HIS 0.005 0.001 HIS R 272 PHE 0.021 0.002 PHE R 187 TYR 0.010 0.001 TYR R 136 ARG 0.002 0.000 ARG R 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.7930 (m-40) cc_final: 0.7203 (t0) REVERT: R 135 PHE cc_start: 0.8204 (t80) cc_final: 0.7499 (t80) REVERT: R 136 TYR cc_start: 0.4921 (m-80) cc_final: 0.4591 (m-80) REVERT: R 254 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7206 (mpp) REVERT: R 268 TRP cc_start: 0.7375 (m100) cc_final: 0.6723 (m100) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.1059 time to fit residues: 5.5614 Evaluate side-chains 46 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.122054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101807 restraints weight = 4713.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104175 restraints weight = 2927.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105377 restraints weight = 2233.660| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1874 Z= 0.185 Angle : 0.747 11.547 2551 Z= 0.336 Chirality : 0.038 0.127 321 Planarity : 0.004 0.025 303 Dihedral : 3.560 11.681 259 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.59 % Allowed : 23.59 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.58), residues: 229 helix: 2.25 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.39 (1.22), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 330 HIS 0.004 0.001 HIS R 272 PHE 0.019 0.002 PHE R 187 TYR 0.011 0.001 TYR R 136 ARG 0.001 0.000 ARG R 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1018.69 seconds wall clock time: 18 minutes 27.62 seconds (1107.62 seconds total)