Starting phenix.real_space_refine on Wed Sep 17 03:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfe_60058/09_2025/8zfe_60058.map" } resolution = 2.56 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1452 2.51 5 N 367 2.21 5 O 367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2198 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2198 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 134 Time building chain proxies: 1.12, per 1000 atoms: 0.51 Number of scatterers: 2198 At special positions: 0 Unit cell: (59.52, 63.24, 71.61, 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 12 16.00 O 367 8.00 N 367 7.00 C 1452 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: 0.20 Conformation dependent library (CDL) restraints added in 91.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 1 sheets defined 72.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 24 through 50 Proline residue: R 35 - end of helix removed outlier: 3.737A pdb=" N CYS R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU R 39 " --> pdb=" O PRO R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 removed outlier: 4.211A pdb=" N VAL R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 70 No H-bonds generated for 'chain 'R' and resid 68 through 70' Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.734A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 122 removed outlier: 3.591A pdb=" N ILE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 131 Processing helix chain 'R' and resid 132 through 151 removed outlier: 3.503A pdb=" N ASN R 151 " --> pdb=" O GLU R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.898A pdb=" N PHE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.641A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 211 Processing helix chain 'R' and resid 219 through 253 removed outlier: 3.676A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix Processing helix chain 'R' and resid 266 through 277 Processing helix chain 'R' and resid 279 through 290 Proline residue: R 285 - end of helix removed outlier: 3.859A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'R' and resid 161 through 162 removed outlier: 3.627A pdb=" N PHE R 161 " --> pdb=" O PHE R 169 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 390 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: 0.23 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 329 1.30 - 1.42: 664 1.42 - 1.55: 1253 1.55 - 1.68: 0 1.68 - 1.81: 16 Bond restraints: 2262 Sorted by residual: bond pdb=" C SER R 152 " pdb=" N ALA R 153 " ideal model delta sigma weight residual 1.331 1.529 -0.198 2.07e-02 2.33e+03 9.15e+01 bond pdb=" C HIS R 157 " pdb=" N ASP R 158 " ideal model delta sigma weight residual 1.330 1.414 -0.084 1.32e-02 5.74e+03 4.03e+01 bond pdb=" CA TYR R 165 " pdb=" C TYR R 165 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.23e-02 6.61e+03 3.59e+01 bond pdb=" C TYR R 165 " pdb=" O TYR R 165 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.36e-02 5.41e+03 2.16e+01 bond pdb=" C HIS R 167 " pdb=" O HIS R 167 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.18e-02 7.18e+03 2.00e+01 ... (remaining 2257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 3009 1.91 - 3.82: 73 3.82 - 5.73: 16 5.73 - 7.64: 3 7.64 - 9.55: 1 Bond angle restraints: 3102 Sorted by residual: angle pdb=" N ASN R 166 " pdb=" CA ASN R 166 " pdb=" C ASN R 166 " ideal model delta sigma weight residual 113.38 120.93 -7.55 1.17e+00 7.31e-01 4.16e+01 angle pdb=" C ARG R 164 " pdb=" N TYR R 165 " pdb=" CA TYR R 165 " ideal model delta sigma weight residual 123.17 116.47 6.70 1.49e+00 4.50e-01 2.02e+01 angle pdb=" O PHE R 156 " pdb=" C PHE R 156 " pdb=" N HIS R 157 " ideal model delta sigma weight residual 122.03 126.32 -4.29 1.04e+00 9.25e-01 1.70e+01 angle pdb=" CA PHE R 156 " pdb=" C PHE R 156 " pdb=" N HIS R 157 " ideal model delta sigma weight residual 116.92 113.24 3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" C HIS R 167 " pdb=" CA HIS R 167 " pdb=" CB HIS R 167 " ideal model delta sigma weight residual 109.38 115.74 -6.36 2.03e+00 2.43e-01 9.83e+00 ... (remaining 3097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.71: 1121 11.71 - 23.42: 117 23.42 - 35.13: 44 35.13 - 46.85: 7 46.85 - 58.56: 4 Dihedral angle restraints: 1293 sinusoidal: 425 harmonic: 868 Sorted by residual: dihedral pdb=" CA THR R 216 " pdb=" C THR R 216 " pdb=" N GLU R 217 " pdb=" CA GLU R 217 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO R 22 " pdb=" C PRO R 22 " pdb=" N PRO R 23 " pdb=" CA PRO R 23 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLY R 96 " pdb=" C GLY R 96 " pdb=" N PHE R 97 " pdb=" CA PHE R 97 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 1290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 354 0.106 - 0.213: 7 0.213 - 0.319: 1 0.319 - 0.426: 0 0.426 - 0.532: 2 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ASN R 166 " pdb=" N ASN R 166 " pdb=" C ASN R 166 " pdb=" CB ASN R 166 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA HIS R 167 " pdb=" N HIS R 167 " pdb=" C HIS R 167 " pdb=" CB HIS R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA TYR R 165 " pdb=" N TYR R 165 " pdb=" C TYR R 165 " pdb=" CB TYR R 165 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 361 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 153 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ALA R 153 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA R 153 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 154 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 153 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 154 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 154 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 154 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 164 " 0.009 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG R 164 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG R 164 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR R 165 " 0.012 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 633 2.80 - 3.33: 2193 3.33 - 3.85: 3690 3.85 - 4.38: 4116 4.38 - 4.90: 7028 Nonbonded interactions: 17660 Sorted by model distance: nonbonded pdb=" O VAL R 32 " pdb=" OG1 THR R 36 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG R 249 " pdb=" OE1 GLU R 263 " model vdw 2.345 3.120 nonbonded pdb=" NE ARG R 249 " pdb=" OE2 GLU R 263 " model vdw 2.430 3.120 nonbonded pdb=" N ASP R 83 " pdb=" OD1 ASP R 83 " model vdw 2.439 3.120 nonbonded pdb=" O SER R 278 " pdb=" OG SER R 278 " model vdw 2.472 3.040 ... (remaining 17655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.008 0.198 2262 Z= 0.419 Angle : 0.764 9.546 3102 Z= 0.439 Chirality : 0.061 0.532 364 Planarity : 0.006 0.063 384 Dihedral : 12.272 58.557 731 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.48 % Allowed : 0.95 % Favored : 98.57 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.33 % 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: -2.16 (0.47), residues: 291 helix: -0.56 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -3.35 (0.52), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 126 TYR 0.010 0.002 TYR R 104 PHE 0.009 0.001 PHE R 267 TRP 0.009 0.001 TRP R 85 HIS 0.015 0.002 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00787 ( 2262) covalent geometry : angle 0.76415 ( 3102) hydrogen bonds : bond 0.16893 ( 131) hydrogen bonds : angle 6.24623 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.087 Fit side-chains REVERT: R 292 ASN cc_start: 0.8133 (p0) cc_final: 0.7916 (p0) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.4261 time to fit residues: 16.2684 Evaluate side-chains 31 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 26 optimal weight: 0.4980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105447 restraints weight = 3447.480| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.67 r_work: 0.3490 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2262 Z= 0.145 Angle : 0.617 7.821 3102 Z= 0.318 Chirality : 0.043 0.135 364 Planarity : 0.004 0.040 384 Dihedral : 5.264 21.155 317 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.90 % Allowed : 12.38 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.43 (0.49), residues: 291 helix: 0.00 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.40 (0.56), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 46 TYR 0.023 0.002 TYR R 270 PHE 0.008 0.001 PHE R 267 TRP 0.005 0.001 TRP R 75 HIS 0.010 0.002 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2262) covalent geometry : angle 0.61740 ( 3102) hydrogen bonds : bond 0.03900 ( 131) hydrogen bonds : angle 4.32038 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.086 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.5390 time to fit residues: 16.0623 Evaluate side-chains 26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.0870 overall best weight: 0.1162 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108632 restraints weight = 3389.663| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.65 r_work: 0.3540 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2262 Z= 0.102 Angle : 0.558 6.542 3102 Z= 0.287 Chirality : 0.040 0.125 364 Planarity : 0.004 0.028 384 Dihedral : 4.679 19.822 317 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.86 % Allowed : 13.33 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.99 (0.50), residues: 291 helix: 0.35 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.32 (0.56), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 46 TYR 0.024 0.001 TYR R 270 PHE 0.006 0.001 PHE R 99 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 2262) covalent geometry : angle 0.55778 ( 3102) hydrogen bonds : bond 0.02890 ( 131) hydrogen bonds : angle 3.91653 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.082 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.5550 time to fit residues: 16.4979 Evaluate side-chains 22 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105934 restraints weight = 3439.260| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.61 r_work: 0.3499 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2262 Z= 0.137 Angle : 0.583 6.152 3102 Z= 0.296 Chirality : 0.041 0.130 364 Planarity : 0.004 0.034 384 Dihedral : 4.695 19.794 317 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.86 % Allowed : 16.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.90 (0.50), residues: 291 helix: 0.39 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.21 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.024 0.001 TYR R 270 PHE 0.008 0.001 PHE R 109 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 123 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2262) covalent geometry : angle 0.58300 ( 3102) hydrogen bonds : bond 0.03229 ( 131) hydrogen bonds : angle 3.87813 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.109 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.6214 time to fit residues: 18.4360 Evaluate side-chains 26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105479 restraints weight = 3480.123| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.62 r_work: 0.3491 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2262 Z= 0.135 Angle : 0.582 5.660 3102 Z= 0.296 Chirality : 0.041 0.128 364 Planarity : 0.004 0.034 384 Dihedral : 4.688 19.917 317 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.33 % Allowed : 16.19 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.79 (0.50), residues: 291 helix: 0.45 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.10 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.025 0.002 TYR R 270 PHE 0.008 0.001 PHE R 109 TRP 0.007 0.001 TRP R 75 HIS 0.003 0.001 HIS R 123 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2262) covalent geometry : angle 0.58234 ( 3102) hydrogen bonds : bond 0.03227 ( 131) hydrogen bonds : angle 3.83498 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.085 Fit side-chains REVERT: R 176 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.5289 (ppp) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.5698 time to fit residues: 16.9499 Evaluate side-chains 27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 27 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 0.1490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS ** R 243 HIS ** 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 = 0.3731 r_free = 0.3731 target = 0.116702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107569 restraints weight = 3339.193| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.63 r_work: 0.3526 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2262 Z= 0.102 Angle : 0.554 6.207 3102 Z= 0.281 Chirality : 0.040 0.123 364 Planarity : 0.004 0.031 384 Dihedral : 4.427 19.084 317 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.33 % Allowed : 16.19 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.51 (0.51), residues: 291 helix: 0.65 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.02 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 46 TYR 0.026 0.001 TYR R 270 PHE 0.007 0.001 PHE R 99 TRP 0.006 0.001 TRP R 75 HIS 0.002 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 2262) covalent geometry : angle 0.55373 ( 3102) hydrogen bonds : bond 0.02808 ( 131) hydrogen bonds : angle 3.70335 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.065 Fit side-chains REVERT: R 110 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7349 (mt) REVERT: R 176 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.5237 (ppp) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.5473 time to fit residues: 16.7956 Evaluate side-chains 28 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104868 restraints weight = 3422.318| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.63 r_work: 0.3484 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2262 Z= 0.155 Angle : 0.594 6.398 3102 Z= 0.303 Chirality : 0.042 0.131 364 Planarity : 0.004 0.038 384 Dihedral : 4.682 20.032 317 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.81 % Allowed : 15.24 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.55 (0.50), residues: 291 helix: 0.58 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.91 (0.64), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.026 0.002 TYR R 270 PHE 0.010 0.001 PHE R 109 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2262) covalent geometry : angle 0.59446 ( 3102) hydrogen bonds : bond 0.03348 ( 131) hydrogen bonds : angle 3.82692 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.085 Fit side-chains REVERT: R 176 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.5357 (ppp) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.5778 time to fit residues: 17.1850 Evaluate side-chains 27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0270 chunk 14 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106446 restraints weight = 3378.997| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.62 r_work: 0.3511 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2262 Z= 0.122 Angle : 0.580 6.082 3102 Z= 0.295 Chirality : 0.041 0.127 364 Planarity : 0.004 0.036 384 Dihedral : 4.550 19.564 317 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.37 (0.51), residues: 291 helix: 0.72 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.83 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.026 0.001 TYR R 270 PHE 0.008 0.001 PHE R 109 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2262) covalent geometry : angle 0.57986 ( 3102) hydrogen bonds : bond 0.03023 ( 131) hydrogen bonds : angle 3.75653 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.051 Fit side-chains REVERT: R 176 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.5341 (ppp) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.5671 time to fit residues: 15.0795 Evaluate side-chains 28 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106563 restraints weight = 3413.498| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.59 r_work: 0.3512 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2262 Z= 0.132 Angle : 0.585 6.117 3102 Z= 0.298 Chirality : 0.041 0.128 364 Planarity : 0.004 0.036 384 Dihedral : 4.558 19.647 317 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.33 % Allowed : 17.14 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.34 (0.51), residues: 291 helix: 0.74 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.82 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.026 0.002 TYR R 270 PHE 0.008 0.001 PHE R 109 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2262) covalent geometry : angle 0.58463 ( 3102) hydrogen bonds : bond 0.03134 ( 131) hydrogen bonds : angle 3.74965 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.066 Fit side-chains REVERT: R 110 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7353 (mt) REVERT: R 176 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.5237 (ppp) outliers start: 7 outliers final: 5 residues processed: 29 average time/residue: 0.4909 time to fit residues: 14.6017 Evaluate side-chains 30 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 0.0270 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105971 restraints weight = 3403.215| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.66 r_work: 0.3504 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2262 Z= 0.138 Angle : 0.596 6.179 3102 Z= 0.304 Chirality : 0.042 0.129 364 Planarity : 0.004 0.037 384 Dihedral : 4.599 19.746 317 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.35 (0.51), residues: 291 helix: 0.72 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.80 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 46 TYR 0.025 0.001 TYR R 270 PHE 0.015 0.001 PHE R 156 TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 123 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2262) covalent geometry : angle 0.59603 ( 3102) hydrogen bonds : bond 0.03172 ( 131) hydrogen bonds : angle 3.73673 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.092 Fit side-chains REVERT: R 110 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7325 (mt) REVERT: R 249 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7741 (mtp180) REVERT: R 263 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8086 (mm-30) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.5495 time to fit residues: 15.2159 Evaluate side-chains 29 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107203 restraints weight = 3506.466| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.63 r_work: 0.3518 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2262 Z= 0.123 Angle : 0.587 6.033 3102 Z= 0.299 Chirality : 0.041 0.127 364 Planarity : 0.004 0.036 384 Dihedral : 4.505 19.491 317 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.33 % Allowed : 17.14 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.30 (0.51), residues: 291 helix: 0.76 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.79 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 46 TYR 0.025 0.001 TYR R 270 PHE 0.014 0.001 PHE R 156 TRP 0.005 0.001 TRP R 75 HIS 0.003 0.001 HIS R 123 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 2262) covalent geometry : angle 0.58680 ( 3102) hydrogen bonds : bond 0.03022 ( 131) hydrogen bonds : angle 3.67657 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.00 seconds wall clock time: 18 minutes 56.42 seconds (1136.42 seconds total)