Starting phenix.real_space_refine on Fri Oct 10 10:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbi_38219/10_2025/8xbi_38219.cif" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= -0.028 sd= 0.435 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 22 5.16 5 C 1641 2.51 5 N 399 2.21 5 O 404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2467 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.03, per 1000 atoms: 0.42 Number of scatterers: 2467 At special positions: 0 Unit cell: (64.55, 73.587, 77.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 1 15.00 O 404 8.00 N 399 7.00 C 1641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.08 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: 0.23 Conformation dependent library (CDL) restraints added in 95.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 84.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 50 through 82 removed outlier: 3.686A pdb=" N ILE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 Proline residue: R 108 - end of helix removed outlier: 4.189A pdb=" N GLN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.561A pdb=" N CYS R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 197 removed outlier: 3.702A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 4.088A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 294 Proline residue: R 281 - end of helix removed outlier: 3.919A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.809A pdb=" N LYS R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.641A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 196 hydrogen bonds defined for protein. 588 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: 0.37 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 623 1.33 - 1.45: 447 1.45 - 1.58: 1417 1.58 - 1.71: 2 1.71 - 1.83: 34 Bond restraints: 2523 Sorted by residual: bond pdb=" C ALA R 265 " pdb=" O ALA R 265 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.17e-02 7.31e+03 1.61e+01 bond pdb=" N ILE R 82 " pdb=" CA ILE R 82 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" C ILE R 270 " pdb=" O ILE R 270 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.13e-02 7.83e+03 1.23e+01 bond pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 ... (remaining 2518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 3148 2.12 - 4.25: 248 4.25 - 6.37: 9 6.37 - 8.49: 1 8.49 - 10.61: 1 Bond angle restraints: 3407 Sorted by residual: angle pdb=" O GLN R 161 " pdb=" C GLN R 161 " pdb=" N GLN R 162 " ideal model delta sigma weight residual 121.76 126.04 -4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" CB GLU R 303 " ideal model delta sigma weight residual 110.16 115.17 -5.01 1.48e+00 4.57e-01 1.14e+01 angle pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " pdb=" NZ LYS R 254 " ideal model delta sigma weight residual 111.90 101.29 10.61 3.20e+00 9.77e-02 1.10e+01 angle pdb=" CG LYS R 254 " pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " ideal model delta sigma weight residual 111.30 118.44 -7.14 2.30e+00 1.89e-01 9.63e+00 angle pdb=" N ILE R 166 " pdb=" CA ILE R 166 " pdb=" C ILE R 166 " ideal model delta sigma weight residual 112.17 109.26 2.91 9.50e-01 1.11e+00 9.39e+00 ... (remaining 3402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 1414 24.76 - 49.51: 83 49.51 - 74.27: 8 74.27 - 99.02: 6 99.02 - 123.78: 3 Dihedral angle restraints: 1514 sinusoidal: 632 harmonic: 882 Sorted by residual: dihedral pdb=" O2 KW3 R 401 " pdb=" C4 KW3 R 401 " pdb=" C5 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 296.46 172.68 123.78 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" N1 KW3 R 401 " pdb=" C28 KW3 R 401 " pdb=" C29 KW3 R 401 " pdb=" O9 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 57.01 -55.00 112.01 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " pdb=" O1 KW3 R 401 " pdb=" C3 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 71.30 -178.59 -110.11 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 1511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 163 0.038 - 0.075: 119 0.075 - 0.113: 66 0.113 - 0.150: 43 0.150 - 0.188: 10 Chirality restraints: 401 Sorted by residual: chirality pdb=" CA ILE R 148 " pdb=" N ILE R 148 " pdb=" C ILE R 148 " pdb=" CB ILE R 148 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE R 156 " pdb=" N ILE R 156 " pdb=" C ILE R 156 " pdb=" CB ILE R 156 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE R 98 " pdb=" N ILE R 98 " pdb=" C ILE R 98 " pdb=" CB ILE R 98 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 398 not shown) Planarity restraints: 399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 269 " 0.039 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE R 269 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE R 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 269 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 269 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE R 269 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 269 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 238 " 0.032 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR R 238 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 238 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR R 238 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 238 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 238 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR R 238 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR R 238 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 279 " 0.024 2.00e-02 2.50e+03 2.21e-02 8.53e+00 pdb=" CG PHE R 279 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 279 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 279 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE R 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 396 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 186 2.76 - 3.29: 2780 3.29 - 3.83: 3984 3.83 - 4.36: 4780 4.36 - 4.90: 8162 Nonbonded interactions: 19892 Sorted by model distance: nonbonded pdb=" OH TYR R 282 " pdb=" NH2 ARG R 286 " model vdw 2.221 3.120 nonbonded pdb=" O LYS R 155 " pdb=" OG SER R 159 " model vdw 2.232 3.040 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.239 3.040 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.276 3.040 nonbonded pdb=" O VAL R 78 " pdb=" ND1 HIS R 83 " model vdw 2.339 3.120 ... (remaining 19887 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: 0.030 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.050 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: 6.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.013 0.056 2525 Z= 0.934 Angle : 1.206 10.611 3411 Z= 0.876 Chirality : 0.071 0.188 401 Planarity : 0.006 0.027 399 Dihedral : 16.804 123.776 938 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.92 (0.45), residues: 296 helix: 2.03 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.99 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG R 110 TYR 0.045 0.008 TYR R 238 PHE 0.053 0.007 PHE R 269 TRP 0.021 0.006 TRP R 179 HIS 0.007 0.002 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.01281 ( 2523) covalent geometry : angle 1.20601 ( 3407) SS BOND : bond 0.03479 ( 2) SS BOND : angle 1.31959 ( 4) hydrogen bonds : bond 0.10752 ( 196) hydrogen bonds : angle 4.74204 ( 588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: R 247 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.6991 (tpp-160) REVERT: R 251 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6919 (ptt180) REVERT: R 303 GLU cc_start: 0.7252 (pm20) cc_final: 0.6944 (pt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0828 time to fit residues: 6.1832 Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.205678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.171977 restraints weight = 2615.349| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.58 r_work: 0.3659 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2525 Z= 0.166 Angle : 0.581 5.594 3411 Z= 0.317 Chirality : 0.041 0.145 401 Planarity : 0.004 0.036 399 Dihedral : 15.905 121.986 363 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 10.55 % Favored : 86.91 % 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 (0.46), residues: 296 helix: 2.05 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.08 (0.63), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 286 TYR 0.012 0.002 TYR R 139 PHE 0.017 0.002 PHE R 227 TRP 0.007 0.001 TRP R 228 HIS 0.005 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2523) covalent geometry : angle 0.58073 ( 3407) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.54146 ( 4) hydrogen bonds : bond 0.05007 ( 196) hydrogen bonds : angle 3.95326 ( 588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.096 Fit side-chains REVERT: R 51 LYS cc_start: 0.7281 (mppt) cc_final: 0.6784 (tttt) REVERT: R 318 PHE cc_start: 0.7435 (t80) cc_final: 0.7155 (t80) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.0767 time to fit residues: 5.7982 Evaluate side-chains 60 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.205176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.174517 restraints weight = 2657.235| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.46 r_work: 0.3705 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2525 Z= 0.130 Angle : 0.499 5.116 3411 Z= 0.279 Chirality : 0.039 0.138 401 Planarity : 0.003 0.026 399 Dihedral : 15.988 125.530 363 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.18 % Allowed : 14.18 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.47), residues: 296 helix: 2.17 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -2.01 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 286 TYR 0.012 0.001 TYR R 139 PHE 0.012 0.001 PHE R 227 TRP 0.007 0.001 TRP R 301 HIS 0.004 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2523) covalent geometry : angle 0.49931 ( 3407) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.40904 ( 4) hydrogen bonds : bond 0.04513 ( 196) hydrogen bonds : angle 3.82984 ( 588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.086 Fit side-chains REVERT: R 51 LYS cc_start: 0.7226 (mppt) cc_final: 0.7015 (tttt) REVERT: R 272 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7732 (tp) REVERT: R 318 PHE cc_start: 0.7538 (t80) cc_final: 0.7223 (t80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.0732 time to fit residues: 5.3350 Evaluate side-chains 61 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.205357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169541 restraints weight = 2659.379| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.69 r_work: 0.3672 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2525 Z= 0.124 Angle : 0.499 4.998 3411 Z= 0.276 Chirality : 0.039 0.129 401 Planarity : 0.003 0.025 399 Dihedral : 15.816 125.747 363 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.27 % Allowed : 16.00 % Favored : 80.73 % 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: 1.99 (0.47), residues: 296 helix: 2.15 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -2.00 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.013 0.001 TYR R 139 PHE 0.011 0.001 PHE R 227 TRP 0.006 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2523) covalent geometry : angle 0.49886 ( 3407) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.36458 ( 4) hydrogen bonds : bond 0.04350 ( 196) hydrogen bonds : angle 3.84983 ( 588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.093 Fit side-chains REVERT: R 167 THR cc_start: 0.5866 (OUTLIER) cc_final: 0.5635 (p) REVERT: R 272 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7713 (tp) REVERT: R 318 PHE cc_start: 0.7418 (t80) cc_final: 0.7083 (t80) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.0690 time to fit residues: 5.4063 Evaluate side-chains 61 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.211694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.176995 restraints weight = 2595.537| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.61 r_work: 0.3716 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2525 Z= 0.120 Angle : 0.492 4.872 3411 Z= 0.271 Chirality : 0.039 0.122 401 Planarity : 0.003 0.024 399 Dihedral : 15.553 123.560 363 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 18.55 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.47), residues: 296 helix: 2.20 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.98 (0.59), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.013 0.001 TYR R 282 PHE 0.011 0.001 PHE R 227 TRP 0.006 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 2523) covalent geometry : angle 0.49202 ( 3407) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.46149 ( 4) hydrogen bonds : bond 0.04192 ( 196) hydrogen bonds : angle 3.82223 ( 588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.055 Fit side-chains REVERT: R 167 THR cc_start: 0.5856 (OUTLIER) cc_final: 0.5643 (p) REVERT: R 272 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7650 (tp) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.0609 time to fit residues: 4.3480 Evaluate side-chains 59 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.205684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.174150 restraints weight = 2637.389| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.49 r_work: 0.3695 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2525 Z= 0.131 Angle : 0.513 5.069 3411 Z= 0.278 Chirality : 0.040 0.131 401 Planarity : 0.003 0.023 399 Dihedral : 15.601 121.760 363 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 19.64 % Favored : 77.45 % 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: 1.97 (0.47), residues: 296 helix: 2.13 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.97 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.016 0.001 TYR R 282 PHE 0.014 0.001 PHE R 227 TRP 0.004 0.001 TRP R 228 HIS 0.003 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2523) covalent geometry : angle 0.51337 ( 3407) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.60232 ( 4) hydrogen bonds : bond 0.04452 ( 196) hydrogen bonds : angle 3.81192 ( 588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7754 (tp) REVERT: R 315 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8176 (tt) REVERT: R 318 PHE cc_start: 0.7627 (t80) cc_final: 0.7290 (t80) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.0656 time to fit residues: 4.6291 Evaluate side-chains 59 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.206689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.171827 restraints weight = 2627.029| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.62 r_work: 0.3657 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2525 Z= 0.134 Angle : 0.506 5.049 3411 Z= 0.276 Chirality : 0.040 0.130 401 Planarity : 0.003 0.023 399 Dihedral : 15.612 122.044 363 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 19.27 % Favored : 78.18 % 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: 1.91 (0.47), residues: 296 helix: 2.07 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.91 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.016 0.001 TYR R 282 PHE 0.014 0.001 PHE R 227 TRP 0.005 0.001 TRP R 228 HIS 0.003 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2523) covalent geometry : angle 0.50640 ( 3407) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.44913 ( 4) hydrogen bonds : bond 0.04508 ( 196) hydrogen bonds : angle 3.80665 ( 588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.070 Fit side-chains REVERT: R 272 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7716 (tp) REVERT: R 315 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8073 (tt) REVERT: R 318 PHE cc_start: 0.7536 (t80) cc_final: 0.7178 (t80) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0783 time to fit residues: 5.2140 Evaluate side-chains 58 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 0.0170 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.204753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.172892 restraints weight = 2650.803| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.49 r_work: 0.3646 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2525 Z= 0.156 Angle : 0.563 5.874 3411 Z= 0.304 Chirality : 0.042 0.132 401 Planarity : 0.004 0.029 399 Dihedral : 15.949 122.926 363 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.91 % Allowed : 19.64 % Favored : 77.45 % 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: 1.64 (0.47), residues: 296 helix: 1.85 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.94 (0.63), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 286 TYR 0.020 0.002 TYR R 282 PHE 0.018 0.002 PHE R 227 TRP 0.005 0.001 TRP R 228 HIS 0.003 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2523) covalent geometry : angle 0.56273 ( 3407) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.58090 ( 4) hydrogen bonds : bond 0.04940 ( 196) hydrogen bonds : angle 3.97122 ( 588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.055 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8244 (tp) REVERT: R 318 PHE cc_start: 0.7735 (t80) cc_final: 0.7369 (t80) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.0545 time to fit residues: 3.7876 Evaluate side-chains 60 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.206804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.171890 restraints weight = 2651.635| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.63 r_work: 0.3654 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2525 Z= 0.136 Angle : 0.530 5.411 3411 Z= 0.292 Chirality : 0.041 0.161 401 Planarity : 0.003 0.023 399 Dihedral : 15.716 123.418 363 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 19.27 % Favored : 78.18 % 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: 1.76 (0.47), residues: 296 helix: 1.93 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.81 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.020 0.001 TYR R 282 PHE 0.013 0.001 PHE R 227 TRP 0.008 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2523) covalent geometry : angle 0.53057 ( 3407) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.44291 ( 4) hydrogen bonds : bond 0.04577 ( 196) hydrogen bonds : angle 3.93872 ( 588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8188 (tp) REVERT: R 318 PHE cc_start: 0.7693 (t80) cc_final: 0.7346 (t80) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.0534 time to fit residues: 3.7671 Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.210039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173849 restraints weight = 2682.190| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.73 r_work: 0.3661 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2525 Z= 0.126 Angle : 0.508 4.906 3411 Z= 0.281 Chirality : 0.041 0.162 401 Planarity : 0.003 0.023 399 Dihedral : 15.400 120.670 363 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.18 % Allowed : 20.36 % Favored : 77.45 % 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: 1.91 (0.47), residues: 296 helix: 2.03 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.75 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 286 TYR 0.018 0.001 TYR R 282 PHE 0.012 0.001 PHE R 227 TRP 0.007 0.001 TRP R 120 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 2523) covalent geometry : angle 0.50837 ( 3407) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.42142 ( 4) hydrogen bonds : bond 0.04298 ( 196) hydrogen bonds : angle 3.91052 ( 588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 120 TRP cc_start: 0.7096 (t-100) cc_final: 0.6650 (t-100) REVERT: R 272 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8069 (tp) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.0560 time to fit residues: 3.9824 Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.206715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172101 restraints weight = 2687.407| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.63 r_work: 0.3674 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2525 Z= 0.128 Angle : 0.518 4.954 3411 Z= 0.283 Chirality : 0.041 0.152 401 Planarity : 0.003 0.027 399 Dihedral : 15.308 118.494 363 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.18 % Allowed : 20.36 % Favored : 77.45 % 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: 1.90 (0.47), residues: 296 helix: 2.01 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.70 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 286 TYR 0.018 0.001 TYR R 282 PHE 0.013 0.001 PHE R 227 TRP 0.006 0.001 TRP R 120 HIS 0.003 0.001 HIS R 206 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2523) covalent geometry : angle 0.51805 ( 3407) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.40676 ( 4) hydrogen bonds : bond 0.04342 ( 196) hydrogen bonds : angle 3.89953 ( 588) =============================================================================== Job complete usr+sys time: 791.01 seconds wall clock time: 14 minutes 12.83 seconds (852.83 seconds total)