Starting phenix.real_space_refine on Wed Sep 17 02:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxy_38765/09_2025/8xxy_38765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxy_38765/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xxy_38765/09_2025/8xxy_38765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxy_38765/09_2025/8xxy_38765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xxy_38765/09_2025/8xxy_38765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxy_38765/09_2025/8xxy_38765.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.59, per 1000 atoms: 0.32 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: 0.11 Conformation dependent library (CDL) restraints added in 49.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.03 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: 0.15 Time building geometry restraints manager: 0.15 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: 0.670 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.900 Find NCS groups from input model: 0.000 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.380 ------------------------------------------------------------------------------- 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= 0.118 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 : 2.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG R 249 TYR 0.004 0.001 TYR R 233 PHE 0.003 0.001 PHE R 147 TRP 0.005 0.001 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 1874) covalent geometry : angle 0.47361 ( 2551) hydrogen bonds : bond 0.19393 ( 158) hydrogen bonds : angle 5.77294 ( 474) *********************** 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 : 0.037 Fit side-chains revert: symmetry clash REVERT: R 86 SER cc_start: 0.9025 (t) cc_final: 0.8276 (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: 0.6633 (t80) REVERT: R 268 TRP cc_start: 0.7383 (m100) cc_final: 0.6710 (m100) REVERT: R 278 ASP cc_start: 0.8258 (t70) cc_final: 0.7890 (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: 0.0419 time to fit residues: 3.5945 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 : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.123086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100478 restraints weight = 4706.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102912 restraints weight = 2977.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104439 restraints weight = 2309.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104927 restraints weight = 2006.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105574 restraints weight = 1889.313| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1874 Z= 0.144 Angle : 0.673 11.759 2551 Z= 0.312 Chirality : 0.038 0.136 321 Planarity : 0.004 0.031 303 Dihedral : 3.527 14.471 259 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.57), residues: 229 helix: 2.16 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.45 (0.98), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 167 TYR 0.014 0.002 TYR R 136 PHE 0.020 0.002 PHE R 131 TRP 0.008 0.001 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 1874) covalent geometry : angle 0.67297 ( 2551) hydrogen bonds : bond 0.04456 ( 158) hydrogen bonds : angle 4.31787 ( 474) *********************** 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 66 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.039 Fit side-chains REVERT: R 135 PHE cc_start: 0.8253 (t80) cc_final: 0.7519 (t80) REVERT: R 216 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8151 (mtm-85) REVERT: R 239 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8876 (mt) REVERT: R 268 TRP cc_start: 0.7305 (m100) cc_final: 0.6695 (m100) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.0236 time to fit residues: 1.8780 Evaluate side-chains 44 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 239 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 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.119390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097466 restraints weight = 5056.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099756 restraints weight = 3146.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101235 restraints weight = 2439.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.101843 restraints weight = 2100.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102393 restraints weight = 1951.541| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1874 Z= 0.178 Angle : 0.734 10.825 2551 Z= 0.339 Chirality : 0.041 0.133 321 Planarity : 0.004 0.026 303 Dihedral : 3.568 12.106 259 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 6.15 % Allowed : 26.15 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.56), residues: 229 helix: 1.68 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.88 (1.16), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 167 TYR 0.015 0.002 TYR R 136 PHE 0.016 0.002 PHE R 131 TRP 0.003 0.001 TRP R 268 HIS 0.004 0.002 HIS R 237 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 1874) covalent geometry : angle 0.73359 ( 2551) hydrogen bonds : bond 0.04723 ( 158) hydrogen bonds : angle 4.43154 ( 474) *********************** 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 55 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.042 Fit side-chains revert: symmetry clash REVERT: R 132 ASN cc_start: 0.8080 (m-40) cc_final: 0.7835 (m-40) REVERT: R 135 PHE cc_start: 0.8279 (t80) cc_final: 0.7612 (t80) REVERT: R 268 TRP cc_start: 0.7323 (m100) cc_final: 0.6714 (m100) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.0242 time to fit residues: 1.5842 Evaluate side-chains 47 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.122401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101006 restraints weight = 4757.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103383 restraints weight = 2923.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104946 restraints weight = 2250.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105643 restraints weight = 1936.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.106001 restraints weight = 1790.688| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5597 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= 0.134 Angle : 0.735 14.046 2551 Z= 0.318 Chirality : 0.038 0.123 321 Planarity : 0.003 0.024 303 Dihedral : 3.646 14.616 259 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 5.13 % Allowed : 25.13 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.58), residues: 229 helix: 1.87 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.74 (1.19), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.013 0.002 TYR R 136 PHE 0.015 0.001 PHE R 131 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 1874) covalent geometry : angle 0.73546 ( 2551) hydrogen bonds : bond 0.03961 ( 158) hydrogen bonds : angle 4.17096 ( 474) *********************** 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 55 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: R 102 LEU cc_start: 0.8720 (tp) cc_final: 0.8462 (tt) REVERT: R 135 PHE cc_start: 0.8314 (t80) cc_final: 0.7542 (t80) REVERT: R 245 SER cc_start: 0.7629 (p) cc_final: 0.7221 (t) REVERT: R 268 TRP cc_start: 0.7308 (m100) cc_final: 0.6604 (m100) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.0227 time to fit residues: 1.4746 Evaluate side-chains 50 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.039 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.121954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100375 restraints weight = 4759.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102865 restraints weight = 2950.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104183 restraints weight = 2255.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105106 restraints weight = 1958.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105106 restraints weight = 1799.088| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1874 Z= 0.132 Angle : 0.734 11.589 2551 Z= 0.321 Chirality : 0.040 0.164 321 Planarity : 0.003 0.024 303 Dihedral : 3.603 13.509 259 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 6.67 % Allowed : 23.59 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.58), residues: 229 helix: 2.00 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.75 (1.23), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.009 0.001 TYR R 136 PHE 0.011 0.001 PHE R 131 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1874) covalent geometry : angle 0.73406 ( 2551) hydrogen bonds : bond 0.04091 ( 158) hydrogen bonds : angle 4.11439 ( 474) *********************** 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: 13 poor density : 44 time to evaluate : 0.042 Fit side-chains revert: symmetry clash REVERT: R 102 LEU cc_start: 0.8681 (tp) cc_final: 0.8444 (tt) REVERT: R 135 PHE cc_start: 0.8311 (t80) cc_final: 0.7697 (t80) REVERT: R 254 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: R 268 TRP cc_start: 0.7341 (m100) cc_final: 0.6668 (m100) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.0275 time to fit residues: 1.7967 Evaluate side-chains 52 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.040 ------------------------------------------------------------------------------- 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 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.121787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100448 restraints weight = 4805.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102904 restraints weight = 2924.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104446 restraints weight = 2217.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105196 restraints weight = 1888.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105325 restraints weight = 1736.417| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1874 Z= 0.136 Angle : 0.790 12.409 2551 Z= 0.337 Chirality : 0.040 0.151 321 Planarity : 0.003 0.023 303 Dihedral : 3.591 13.668 259 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.62 % Allowed : 24.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.57), residues: 229 helix: 2.01 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.57 (1.29), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 167 TYR 0.008 0.001 TYR R 136 PHE 0.010 0.001 PHE R 131 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 1874) covalent geometry : angle 0.78993 ( 2551) hydrogen bonds : bond 0.04073 ( 158) hydrogen bonds : angle 4.23004 ( 474) *********************** 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 55 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8293 (t80) cc_final: 0.7717 (t80) REVERT: R 254 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7308 (mpp) REVERT: R 268 TRP cc_start: 0.7328 (m100) cc_final: 0.6622 (m100) REVERT: R 318 TYR cc_start: 0.8768 (m-80) cc_final: 0.8498 (m-80) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.0391 time to fit residues: 2.4936 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 : 0.069 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.122568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102101 restraints weight = 4833.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104431 restraints weight = 3043.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105661 restraints weight = 2348.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106644 restraints weight = 2043.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107003 restraints weight = 1860.883| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1874 Z= 0.130 Angle : 0.826 15.597 2551 Z= 0.343 Chirality : 0.039 0.157 321 Planarity : 0.003 0.024 303 Dihedral : 3.554 14.061 259 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.62 % Allowed : 26.67 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.58), residues: 229 helix: 2.18 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.57 (1.29), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 216 TYR 0.008 0.001 TYR R 318 PHE 0.014 0.002 PHE R 182 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 1874) covalent geometry : angle 0.82638 ( 2551) hydrogen bonds : bond 0.03907 ( 158) hydrogen bonds : angle 4.18362 ( 474) *********************** 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 54 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8201 (t80) cc_final: 0.7705 (t80) REVERT: R 254 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7087 (mpp) REVERT: R 268 TRP cc_start: 0.7253 (m100) cc_final: 0.6537 (m100) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.0416 time to fit residues: 2.6208 Evaluate side-chains 49 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 282 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 314 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 = 0.3857 r_free = 0.3857 target = 0.121543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101027 restraints weight = 4938.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103314 restraints weight = 3186.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104766 restraints weight = 2468.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105624 restraints weight = 2125.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105804 restraints weight = 1944.101| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6363 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= 0.138 Angle : 0.793 13.869 2551 Z= 0.345 Chirality : 0.040 0.198 321 Planarity : 0.003 0.024 303 Dihedral : 3.522 13.304 259 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.62 % Allowed : 29.23 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.58), residues: 229 helix: 2.24 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.57 (1.27), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 149 TYR 0.007 0.001 TYR R 136 PHE 0.048 0.003 PHE R 182 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1874) covalent geometry : angle 0.79285 ( 2551) hydrogen bonds : bond 0.04019 ( 158) hydrogen bonds : angle 4.10181 ( 474) *********************** 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 52 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8262 (t80) cc_final: 0.7754 (t80) REVERT: R 254 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: R 268 TRP cc_start: 0.7275 (m100) cc_final: 0.6571 (m100) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.0421 time to fit residues: 2.5000 Evaluate side-chains 51 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 151 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 Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.120787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100205 restraints weight = 4995.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102632 restraints weight = 3068.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103963 restraints weight = 2337.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105087 restraints weight = 2016.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105304 restraints weight = 1811.811| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1874 Z= 0.153 Angle : 0.877 14.781 2551 Z= 0.374 Chirality : 0.040 0.162 321 Planarity : 0.004 0.026 303 Dihedral : 3.584 13.988 259 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.15 % Allowed : 27.69 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.57), residues: 229 helix: 2.20 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.99 (1.17), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 149 TYR 0.007 0.001 TYR R 136 PHE 0.051 0.003 PHE R 182 TRP 0.002 0.000 TRP R 268 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 1874) covalent geometry : angle 0.87691 ( 2551) hydrogen bonds : bond 0.04189 ( 158) hydrogen bonds : angle 4.26585 ( 474) *********************** 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 55 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: R 135 PHE cc_start: 0.8247 (t80) cc_final: 0.7700 (t80) REVERT: R 254 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7297 (mpp) REVERT: R 268 TRP cc_start: 0.7328 (m100) cc_final: 0.6609 (m100) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.0406 time to fit residues: 2.5670 Evaluate side-chains 52 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 151 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 Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP 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 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN 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 = 0.121368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101640 restraints weight = 4816.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103923 restraints weight = 3097.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105372 restraints weight = 2397.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105986 restraints weight = 2058.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105986 restraints weight = 1905.458| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 1874 Z= 0.152 Angle : 0.854 17.842 2551 Z= 0.370 Chirality : 0.041 0.230 321 Planarity : 0.004 0.025 303 Dihedral : 3.512 13.115 259 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 6.67 % Allowed : 27.69 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.57), residues: 229 helix: 2.11 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -2.52 (1.28), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 149 TYR 0.006 0.001 TYR R 150 PHE 0.045 0.003 PHE R 182 TRP 0.003 0.001 TRP R 330 HIS 0.003 0.001 HIS R 237 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 1874) covalent geometry : angle 0.85351 ( 2551) hydrogen bonds : bond 0.04162 ( 158) hydrogen bonds : angle 4.22459 ( 474) ********************** 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 53 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.074 Fit side-chains REVERT: R 135 PHE cc_start: 0.8173 (t80) cc_final: 0.7622 (t80) REVERT: R 219 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6972 (tp-100) REVERT: R 254 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: R 268 TRP cc_start: 0.7316 (m100) cc_final: 0.6658 (m100) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.0476 time to fit residues: 2.8085 Evaluate side-chains 48 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 254 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.121525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101176 restraints weight = 5007.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103636 restraints weight = 3079.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105050 restraints weight = 2342.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105690 restraints weight = 2006.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106352 restraints weight = 1854.780| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1874 Z= 0.142 Angle : 0.888 18.069 2551 Z= 0.387 Chirality : 0.041 0.216 321 Planarity : 0.004 0.026 303 Dihedral : 3.632 14.561 259 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 4.62 % Allowed : 28.72 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.58), residues: 229 helix: 2.00 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -2.45 (1.27), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 216 TYR 0.024 0.002 TYR R 136 PHE 0.047 0.002 PHE R 182 TRP 0.002 0.000 TRP R 268 HIS 0.002 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 1874) covalent geometry : angle 0.88810 ( 2551) hydrogen bonds : bond 0.04107 ( 158) hydrogen bonds : angle 4.27509 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 501.50 seconds wall clock time: 9 minutes 31.52 seconds (571.52 seconds total)