Starting phenix.real_space_refine on Fri Aug 22 12:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggl_40012/08_2025/8ggl_40012.cif" } resolution = 3.2 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= 0.030 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 16 5.16 5 C 1436 2.51 5 N 340 2.21 5 O 359 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2135 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 104 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 0.98, per 1000 atoms: 0.46 Number of scatterers: 2151 At special positions: 0 Unit cell: (56.4005, 82.4315, 61.6067, 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 16 16.00 O 359 8.00 N 340 7.00 C 1436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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 84.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.754A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.252A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.736A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 171 removed outlier: 4.142A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.637A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.936A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 287 Processing helix chain 'R' and resid 288 through 299 removed outlier: 3.661A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 315 removed outlier: 3.549A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 320 Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 341 161 hydrogen bonds defined for protein. 477 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: 0.32 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: 1.21 - 1.33: 362 1.33 - 1.45: 606 1.45 - 1.57: 1215 1.57 - 1.69: 0 1.69 - 1.82: 22 Bond restraints: 2205 Sorted by residual: bond pdb=" C MET R 36 " pdb=" N GLY R 37 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.21e-02 6.83e+03 8.61e+00 bond pdb=" CA MET R 36 " pdb=" C MET R 36 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.39e-02 5.18e+03 8.32e+00 bond pdb=" CA MET R 36 " pdb=" CB MET R 36 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.68e-02 3.54e+03 6.88e+00 bond pdb=" CA VAL R 33 " pdb=" CB VAL R 33 " ideal model delta sigma weight residual 1.540 1.505 0.036 1.36e-02 5.41e+03 6.83e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.27e+00 ... (remaining 2200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 2960 1.69 - 3.39: 45 3.39 - 5.08: 12 5.08 - 6.78: 4 6.78 - 8.47: 1 Bond angle restraints: 3022 Sorted by residual: angle pdb=" N GLY R 35 " pdb=" CA GLY R 35 " pdb=" C GLY R 35 " ideal model delta sigma weight residual 112.73 121.20 -8.47 1.20e+00 6.94e-01 4.99e+01 angle pdb=" C VAL R 34 " pdb=" CA VAL R 34 " pdb=" CB VAL R 34 " ideal model delta sigma weight residual 112.14 105.60 6.54 1.35e+00 5.49e-01 2.35e+01 angle pdb=" CA GLY R 35 " pdb=" C GLY R 35 " pdb=" O GLY R 35 " ideal model delta sigma weight residual 120.75 116.78 3.97 1.03e+00 9.43e-01 1.49e+01 angle pdb=" CA GLY R 35 " pdb=" C GLY R 35 " pdb=" N MET R 36 " ideal model delta sigma weight residual 117.04 120.67 -3.63 9.90e-01 1.02e+00 1.34e+01 angle pdb=" N MET R 36 " pdb=" CA MET R 36 " pdb=" C MET R 36 " ideal model delta sigma weight residual 112.89 108.92 3.97 1.24e+00 6.50e-01 1.02e+01 ... (remaining 3017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 1079 11.10 - 22.21: 116 22.21 - 33.31: 45 33.31 - 44.41: 15 44.41 - 55.52: 5 Dihedral angle restraints: 1260 sinusoidal: 424 harmonic: 836 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB MET R 171 " pdb=" CG MET R 171 " pdb=" SD MET R 171 " pdb=" CE MET R 171 " ideal model delta sinusoidal sigma weight residual 180.00 127.53 52.47 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CG ARG R 328 " pdb=" CD ARG R 328 " pdb=" NE ARG R 328 " pdb=" CZ ARG R 328 " ideal model delta sinusoidal sigma weight residual 180.00 -140.45 -39.55 2 1.50e+01 4.44e-03 8.65e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 219 0.029 - 0.059: 97 0.059 - 0.088: 38 0.088 - 0.117: 19 0.117 - 0.146: 1 Chirality restraints: 374 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL R 33 " pdb=" N VAL R 33 " pdb=" C VAL R 33 " pdb=" CB VAL R 33 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL R 34 " pdb=" N VAL R 34 " pdb=" C VAL R 34 " pdb=" CB VAL R 34 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 ... (remaining 371 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 32 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TRP R 32 " 0.058 2.00e-02 2.50e+03 pdb=" O TRP R 32 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL R 33 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 34 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C VAL R 34 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL R 34 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY R 35 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO R 211 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.024 5.00e-02 4.00e+02 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 652 2.83 - 3.35: 2124 3.35 - 3.86: 3356 3.86 - 4.38: 3610 4.38 - 4.90: 6603 Nonbonded interactions: 16345 Sorted by model distance: nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.312 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.323 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.482 3.040 nonbonded pdb=" O ARG R 175 " pdb=" ND2 ASN R 196 " model vdw 2.589 3.120 nonbonded pdb=" N MET R 36 " pdb=" N GLY R 37 " model vdw 2.602 2.560 ... (remaining 16340 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=0.00 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.760 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.005 0.050 2206 Z= 0.266 Angle : 0.619 8.473 3024 Z= 0.371 Chirality : 0.041 0.146 374 Planarity : 0.004 0.042 360 Dihedral : 12.383 55.517 713 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 1.05 (0.50), residues: 278 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.07 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.008 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 2205) covalent geometry : angle 0.61794 ( 3022) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.30885 ( 2) hydrogen bonds : bond 0.15324 ( 161) hydrogen bonds : angle 5.46665 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.121 Fit side-chains REVERT: R 161 SER cc_start: 0.8768 (m) cc_final: 0.8466 (m) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1139 time to fit residues: 2.9829 Evaluate side-chains 20 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102386 restraints weight = 2816.802| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.48 r_work: 0.2992 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2206 Z= 0.138 Angle : 0.470 5.346 3024 Z= 0.260 Chirality : 0.038 0.102 374 Planarity : 0.004 0.043 360 Dihedral : 4.285 17.822 313 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.35 % Allowed : 5.16 % Favored : 92.49 % 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: 1.40 (0.50), residues: 278 helix: 1.74 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.00 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2205) covalent geometry : angle 0.46940 ( 3022) SS BOND : bond 0.00089 ( 1) SS BOND : angle 1.01455 ( 2) hydrogen bonds : bond 0.06374 ( 161) hydrogen bonds : angle 4.23140 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.084 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1075 time to fit residues: 2.9304 Evaluate side-chains 23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.115654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101479 restraints weight = 2880.411| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.52 r_work: 0.2976 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2206 Z= 0.141 Angle : 0.463 5.356 3024 Z= 0.256 Chirality : 0.038 0.103 374 Planarity : 0.003 0.040 360 Dihedral : 4.258 18.226 313 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.82 % Allowed : 7.51 % Favored : 89.67 % 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: 1.68 (0.49), residues: 278 helix: 2.07 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.75 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.007 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.005 0.001 TRP R 158 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2205) covalent geometry : angle 0.46215 ( 3022) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.05902 ( 2) hydrogen bonds : bond 0.06395 ( 161) hydrogen bonds : angle 4.10589 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.083 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.1016 time to fit residues: 2.8929 Evaluate side-chains 23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098263 restraints weight = 2849.047| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.50 r_work: 0.2933 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2206 Z= 0.173 Angle : 0.498 5.446 3024 Z= 0.275 Chirality : 0.040 0.109 374 Planarity : 0.003 0.040 360 Dihedral : 4.412 18.974 313 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.23 % Allowed : 8.45 % Favored : 87.32 % 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: 1.56 (0.49), residues: 278 helix: 1.95 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.68 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.008 0.001 PHE R 332 TRP 0.005 0.001 TRP R 158 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2205) covalent geometry : angle 0.49723 ( 3022) SS BOND : bond 0.00146 ( 1) SS BOND : angle 1.12488 ( 2) hydrogen bonds : bond 0.07223 ( 161) hydrogen bonds : angle 4.16570 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.083 Fit side-chains REVERT: R 296 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8421 (p-80) outliers start: 9 outliers final: 7 residues processed: 26 average time/residue: 0.1011 time to fit residues: 2.9863 Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100672 restraints weight = 2833.143| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.49 r_work: 0.2967 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2206 Z= 0.139 Angle : 0.458 5.309 3024 Z= 0.253 Chirality : 0.038 0.104 374 Planarity : 0.003 0.037 360 Dihedral : 4.263 18.664 313 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.23 % Allowed : 10.80 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.49), residues: 278 helix: 2.11 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.61 (0.60), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.007 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2205) covalent geometry : angle 0.45782 ( 3022) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.96394 ( 2) hydrogen bonds : bond 0.06484 ( 161) hydrogen bonds : angle 4.03583 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.085 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 27 average time/residue: 0.0966 time to fit residues: 2.9820 Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.114002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100010 restraints weight = 2798.519| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.49 r_work: 0.2958 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2206 Z= 0.141 Angle : 0.459 5.346 3024 Z= 0.253 Chirality : 0.039 0.180 374 Planarity : 0.003 0.036 360 Dihedral : 4.229 18.683 313 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 11.27 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.49), residues: 278 helix: 2.17 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.59 (0.61), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.007 0.001 PHE R 61 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2205) covalent geometry : angle 0.45842 ( 3022) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.96356 ( 2) hydrogen bonds : bond 0.06416 ( 161) hydrogen bonds : angle 4.01706 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.096 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 25 average time/residue: 0.0960 time to fit residues: 2.7710 Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.115632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101645 restraints weight = 2810.489| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.49 r_work: 0.3006 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2206 Z= 0.127 Angle : 0.447 5.297 3024 Z= 0.246 Chirality : 0.038 0.138 374 Planarity : 0.003 0.034 360 Dihedral : 4.120 18.487 313 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.82 % Allowed : 11.27 % Favored : 85.92 % 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: 2.01 (0.50), residues: 278 helix: 2.30 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.55 (0.62), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.006 0.001 TYR R 199 PHE 0.007 0.001 PHE R 217 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2205) covalent geometry : angle 0.44639 ( 3022) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.94275 ( 2) hydrogen bonds : bond 0.05931 ( 161) hydrogen bonds : angle 3.94670 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8688 (m) cc_final: 0.8474 (m) outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.0874 time to fit residues: 2.7162 Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.113836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099962 restraints weight = 2803.434| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.47 r_work: 0.2969 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2206 Z= 0.143 Angle : 0.462 5.356 3024 Z= 0.254 Chirality : 0.039 0.128 374 Planarity : 0.003 0.033 360 Dihedral : 4.192 18.791 313 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.29 % Allowed : 11.74 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.95 (0.50), residues: 278 helix: 2.27 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -1.60 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.007 0.001 PHE R 61 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2205) covalent geometry : angle 0.46155 ( 3022) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.96892 ( 2) hydrogen bonds : bond 0.06361 ( 161) hydrogen bonds : angle 3.98234 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8680 (m) cc_final: 0.8468 (m) outliers start: 7 outliers final: 7 residues processed: 26 average time/residue: 0.0890 time to fit residues: 2.6681 Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.097432 restraints weight = 2871.036| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.48 r_work: 0.2924 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2206 Z= 0.179 Angle : 0.504 5.461 3024 Z= 0.276 Chirality : 0.040 0.125 374 Planarity : 0.003 0.034 360 Dihedral : 4.400 18.992 313 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 11.74 % Favored : 84.51 % 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: 1.53 (0.49), residues: 278 helix: 1.88 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.77 (0.62), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.007 0.001 PHE R 89 TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2205) covalent geometry : angle 0.50336 ( 3022) SS BOND : bond 0.00146 ( 1) SS BOND : angle 1.07759 ( 2) hydrogen bonds : bond 0.07262 ( 161) hydrogen bonds : angle 4.10716 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8708 (m) cc_final: 0.8496 (m) REVERT: R 296 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8427 (p-80) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.0822 time to fit residues: 2.5785 Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101874 restraints weight = 2889.703| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.51 r_work: 0.2984 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2206 Z= 0.119 Angle : 0.442 5.245 3024 Z= 0.244 Chirality : 0.038 0.114 374 Planarity : 0.003 0.030 360 Dihedral : 4.095 18.569 313 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.29 % Allowed : 12.68 % Favored : 84.04 % 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: 2.08 (0.50), residues: 278 helix: 2.35 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.52 (0.62), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.006 0.001 TYR R 199 PHE 0.007 0.001 PHE R 217 TRP 0.006 0.001 TRP R 109 HIS 0.007 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2205) covalent geometry : angle 0.44174 ( 3022) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.90522 ( 2) hydrogen bonds : bond 0.05803 ( 161) hydrogen bonds : angle 3.94110 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8645 (m) cc_final: 0.8439 (m) outliers start: 7 outliers final: 6 residues processed: 29 average time/residue: 0.0851 time to fit residues: 2.8443 Evaluate side-chains 29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.113674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099692 restraints weight = 2912.763| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.51 r_work: 0.2961 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2206 Z= 0.146 Angle : 0.466 5.368 3024 Z= 0.256 Chirality : 0.039 0.115 374 Planarity : 0.003 0.029 360 Dihedral : 4.185 18.806 313 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.82 % Allowed : 12.68 % Favored : 84.51 % 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 (0.50), residues: 278 helix: 2.14 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.48 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.007 0.001 TYR R 199 PHE 0.007 0.001 PHE R 61 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2205) covalent geometry : angle 0.46569 ( 3022) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.98086 ( 2) hydrogen bonds : bond 0.06428 ( 161) hydrogen bonds : angle 3.98948 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 841.79 seconds wall clock time: 15 minutes 8.49 seconds (908.49 seconds total)