Starting phenix.real_space_refine on Tue Aug 4 12:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxp_64589/08_2026/9uxp_64589.map" } resolution = 2.9 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= 0.001 sd= 0.120 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 19 5.16 5 C 1529 2.51 5 N 370 2.21 5 O 391 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2309 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2298 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {'ITN': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.02, per 1000 atoms: 0.44 Number of scatterers: 2309 At special positions: 0 Unit cell: (56.58, 53.3, 73.8, 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 19 16.00 O 391 8.00 N 370 7.00 C 1529 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 183 " distance=2.22 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: 0.25 Conformation dependent library (CDL) restraints added in 99.5 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 85.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'R' and resid 28 through 62 removed outlier: 3.654A pdb=" N LYS R 32 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Proline residue: R 37 - end of helix Proline residue: R 49 - end of helix removed outlier: 3.681A pdb=" N MET R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.008A pdb=" N ILE R 71 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.985A pdb=" N LEU R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.682A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Proline residue: R 167 - end of helix removed outlier: 4.161A pdb=" N PHE R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.720A pdb=" N TRP R 197 " --> pdb=" O ASN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 270 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 293 through 302 Processing helix chain 'R' and resid 306 through 313 Processing sheet with id=AA1, first strand: chain 'R' and resid 173 through 176 removed outlier: 3.943A pdb=" N THR R 173 " --> pdb=" O LEU R 184 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 537 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: 0.30 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 671 1.34 - 1.46: 373 1.46 - 1.57: 1297 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 2366 Sorted by residual: bond pdb=" C ILE R 285 " pdb=" O ILE R 285 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.13e-02 7.83e+03 2.66e+00 bond pdb=" C2 ITN R 401 " pdb=" C3 ITN R 401 " ideal model delta sigma weight residual 1.495 1.527 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C ILE R 29 " pdb=" N PRO R 30 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.38e-01 bond pdb=" CA ILE R 29 " pdb=" C ILE R 29 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.05e-02 9.07e+03 6.75e-01 bond pdb=" C LEU R 86 " pdb=" N PRO R 87 " ideal model delta sigma weight residual 1.335 1.345 -0.011 1.28e-02 6.10e+03 6.73e-01 ... (remaining 2361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 3167 1.96 - 3.91: 42 3.91 - 5.87: 12 5.87 - 7.83: 4 7.83 - 9.78: 1 Bond angle restraints: 3226 Sorted by residual: angle pdb=" CA LEU R 31 " pdb=" CB LEU R 31 " pdb=" CG LEU R 31 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.81e+00 angle pdb=" N ILE R 166 " pdb=" CA ILE R 166 " pdb=" C ILE R 166 " ideal model delta sigma weight residual 108.88 113.80 -4.92 2.16e+00 2.14e-01 5.20e+00 angle pdb=" C ILE R 285 " pdb=" CA ILE R 285 " pdb=" CB ILE R 285 " ideal model delta sigma weight residual 111.97 109.11 2.86 1.28e+00 6.10e-01 5.00e+00 angle pdb=" C LEU R 45 " pdb=" N VAL R 46 " pdb=" CA VAL R 46 " ideal model delta sigma weight residual 120.82 117.36 3.46 1.55e+00 4.16e-01 4.99e+00 angle pdb=" C CYS R 253 " pdb=" N PHE R 254 " pdb=" CA PHE R 254 " ideal model delta sigma weight residual 122.79 118.85 3.94 1.78e+00 3.16e-01 4.89e+00 ... (remaining 3221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1221 17.88 - 35.75: 132 35.75 - 53.63: 30 53.63 - 71.51: 3 71.51 - 89.38: 1 Dihedral angle restraints: 1387 sinusoidal: 531 harmonic: 856 Sorted by residual: dihedral pdb=" CB MET R 139 " pdb=" CG MET R 139 " pdb=" SD MET R 139 " pdb=" CE MET R 139 " ideal model delta sinusoidal sigma weight residual -60.00 -9.33 -50.67 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" N LEU R 209 " pdb=" CA LEU R 209 " pdb=" CB LEU R 209 " pdb=" CG LEU R 209 " ideal model delta sinusoidal sigma weight residual -60.00 -107.19 47.19 3 1.50e+01 4.44e-03 8.45e+00 dihedral pdb=" CG LYS R 196 " pdb=" CD LYS R 196 " pdb=" CE LYS R 196 " pdb=" NZ LYS R 196 " ideal model delta sinusoidal sigma weight residual 180.00 132.92 47.08 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 1384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 265 0.034 - 0.069: 99 0.069 - 0.103: 24 0.103 - 0.137: 5 0.137 - 0.171: 1 Chirality restraints: 394 Sorted by residual: chirality pdb=" CG LEU R 269 " pdb=" CB LEU R 269 " pdb=" CD1 LEU R 269 " pdb=" CD2 LEU R 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE R 285 " pdb=" N ILE R 285 " pdb=" C ILE R 285 " pdb=" CB ILE R 285 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ARG R 63 " pdb=" N ARG R 63 " pdb=" C ARG R 63 " pdb=" CB ARG R 63 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 391 not shown) Planarity restraints: 386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 63 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO R 64 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 64 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO R 210 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 170 " -0.005 2.00e-02 2.50e+03 8.28e-03 1.20e+00 pdb=" CG PHE R 170 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 170 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 170 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 170 " 0.000 2.00e-02 2.50e+03 ... (remaining 383 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 823 2.86 - 3.37: 2383 3.37 - 3.88: 4101 3.88 - 4.39: 4362 4.39 - 4.90: 7782 Nonbonded interactions: 19451 Sorted by model distance: nonbonded pdb=" OD2 ASP R 185 " pdb=" O HOH R 501 " model vdw 2.351 3.040 nonbonded pdb=" O SER R 189 " pdb=" NH2 ARG R 268 " model vdw 2.374 3.120 nonbonded pdb=" O GLU R 97 " pdb=" NE ARG R 180 " model vdw 2.413 3.120 nonbonded pdb=" OH TYR R 93 " pdb=" O4 ITN R 401 " model vdw 2.454 3.040 nonbonded pdb=" O ASP R 190 " pdb=" N LEU R 192 " model vdw 2.495 3.120 ... (remaining 19446 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: 0.820 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.200 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.188 2367 Z= 0.240 Angle : 0.664 9.783 3228 Z= 0.335 Chirality : 0.039 0.171 394 Planarity : 0.004 0.050 386 Dihedral : 15.509 89.382 826 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.38 % Allowed : 16.73 % Favored : 82.89 % 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 are not related in a simple way. whole: 2.35 (0.49), residues: 284 helix: 2.22 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -1.35 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 264 TYR 0.006 0.001 TYR R 198 PHE 0.019 0.001 PHE R 170 TRP 0.005 0.001 TRP R 158 HIS 0.007 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 2366) covalent geometry : angle 0.65262 / 0.33 ( 3226) SS BOND : bond 0.18771 / 9.88 ( 1) SS BOND : angle 5.05715 / 2.71 ( 2) hydrogen bonds : bond 0.07936 / 5.84 ( 179) hydrogen bonds : angle 5.15415 / 3.93 ( 537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.086 Fit side-chains REVERT: R 45 LEU cc_start: 0.7998 (mp) cc_final: 0.7748 (mp) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.5325 time to fit residues: 13.1543 Evaluate side-chains 20 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.0070 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117749 restraints weight = 2570.994| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.41 r_work: 0.3174 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2367 Z= 0.133 Angle : 0.555 7.799 3228 Z= 0.280 Chirality : 0.039 0.128 394 Planarity : 0.005 0.056 386 Dihedral : 7.278 86.304 315 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.18 % Allowed : 14.45 % Favored : 81.37 % 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 are not related in a simple way. whole: 2.08 (0.50), residues: 284 helix: 2.02 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.14 (0.83), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.011 0.001 TYR R 118 PHE 0.013 0.001 PHE R 113 TRP 0.006 0.001 TRP R 158 HIS 0.008 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 2366) covalent geometry : angle 0.55479 / 0.28 ( 3226) SS BOND : bond 0.00644 / 0.34 ( 1) SS BOND : angle 0.22424 / 0.12 ( 2) hydrogen bonds : bond 0.04220 / 2.93 ( 179) hydrogen bonds : angle 4.32654 / 3.25 ( 537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.064 Fit side-chains REVERT: R 33 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7217 (ttp) REVERT: R 168 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8014 (tpp) outliers start: 11 outliers final: 3 residues processed: 25 average time/residue: 0.3343 time to fit residues: 8.6312 Evaluate side-chains 26 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 168 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112373 restraints weight = 2556.849| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.45 r_work: 0.3117 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2367 Z= 0.182 Angle : 0.617 8.396 3228 Z= 0.313 Chirality : 0.042 0.149 394 Planarity : 0.005 0.053 386 Dihedral : 6.757 81.893 313 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.32 % Allowed : 13.69 % Favored : 80.99 % 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 are not related in a simple way. whole: 1.84 (0.49), residues: 284 helix: 1.84 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.08 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.013 0.001 TYR R 118 PHE 0.014 0.002 PHE R 113 TRP 0.009 0.001 TRP R 158 HIS 0.007 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 2366) covalent geometry : angle 0.61687 / 0.31 ( 3226) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 0.11302 / 0.06 ( 2) hydrogen bonds : bond 0.04901 / 3.39 ( 179) hydrogen bonds : angle 4.40943 / 3.33 ( 537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.100 Fit side-chains REVERT: R 33 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7141 (ttp) REVERT: R 90 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 14 outliers final: 6 residues processed: 28 average time/residue: 0.2994 time to fit residues: 8.7561 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 105 MET Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116030 restraints weight = 2586.853| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.42 r_work: 0.3142 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2367 Z= 0.144 Angle : 0.569 8.101 3228 Z= 0.287 Chirality : 0.040 0.138 394 Planarity : 0.005 0.053 386 Dihedral : 6.451 77.748 313 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.18 % Allowed : 14.07 % Favored : 81.75 % 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 are not related in a simple way. whole: 1.90 (0.49), residues: 284 helix: 1.90 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.14 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 148 TYR 0.009 0.001 TYR R 118 PHE 0.013 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.006 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 2366) covalent geometry : angle 0.56919 / 0.29 ( 3226) SS BOND : bond 0.00328 / 0.17 ( 1) SS BOND : angle 0.15616 / 0.09 ( 2) hydrogen bonds : bond 0.04373 / 3.03 ( 179) hydrogen bonds : angle 4.23374 / 3.17 ( 537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.087 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 29 average time/residue: 0.3137 time to fit residues: 9.4573 Evaluate side-chains 26 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115610 restraints weight = 2532.528| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.39 r_work: 0.3125 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2367 Z= 0.157 Angle : 0.586 8.683 3228 Z= 0.296 Chirality : 0.040 0.140 394 Planarity : 0.005 0.053 386 Dihedral : 6.305 73.312 313 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.56 % Allowed : 15.59 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.49), residues: 284 helix: 1.85 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -2.20 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.007 0.001 TYR R 198 PHE 0.013 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.004 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 2366) covalent geometry : angle 0.58602 / 0.30 ( 3226) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 0.07258 / 0.04 ( 2) hydrogen bonds : bond 0.04485 / 3.10 ( 179) hydrogen bonds : angle 4.25954 / 3.19 ( 537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.082 Fit side-chains REVERT: R 33 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7049 (ttp) REVERT: R 90 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8495 (mp) outliers start: 12 outliers final: 6 residues processed: 29 average time/residue: 0.4247 time to fit residues: 12.7446 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 105 MET Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116309 restraints weight = 2544.617| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.40 r_work: 0.3137 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2367 Z= 0.147 Angle : 0.546 6.974 3228 Z= 0.282 Chirality : 0.040 0.138 394 Planarity : 0.004 0.052 386 Dihedral : 5.874 63.663 313 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.94 % Allowed : 14.83 % Favored : 80.23 % 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 are not related in a simple way. whole: 1.88 (0.49), residues: 284 helix: 1.90 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -2.23 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.011 0.001 TYR R 118 PHE 0.013 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 2366) covalent geometry : angle 0.54616 / 0.28 ( 3226) SS BOND : bond 0.00298 / 0.16 ( 1) SS BOND : angle 0.07203 / 0.04 ( 2) hydrogen bonds : bond 0.04379 / 3.03 ( 179) hydrogen bonds : angle 4.23192 / 3.17 ( 537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.087 Fit side-chains REVERT: R 33 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7085 (ttp) REVERT: R 90 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8490 (mp) outliers start: 13 outliers final: 6 residues processed: 29 average time/residue: 0.3859 time to fit residues: 11.5807 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118053 restraints weight = 2548.943| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.41 r_work: 0.3140 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2367 Z= 0.150 Angle : 0.553 7.065 3228 Z= 0.287 Chirality : 0.040 0.138 394 Planarity : 0.005 0.053 386 Dihedral : 5.618 55.629 313 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.94 % Allowed : 15.59 % Favored : 79.47 % 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 are not related in a simple way. whole: 1.89 (0.49), residues: 284 helix: 1.91 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -2.24 (0.85), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.008 0.001 TYR R 118 PHE 0.013 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 2366) covalent geometry : angle 0.55316 / 0.29 ( 3226) SS BOND : bond 0.00262 / 0.14 ( 1) SS BOND : angle 0.04481 / 0.02 ( 2) hydrogen bonds : bond 0.04407 / 3.06 ( 179) hydrogen bonds : angle 4.24967 / 3.19 ( 537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: R 33 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7073 (ttp) REVERT: R 90 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8543 (mp) REVERT: R 206 THR cc_start: 0.8464 (m) cc_final: 0.8217 (m) outliers start: 13 outliers final: 7 residues processed: 29 average time/residue: 0.3792 time to fit residues: 11.3742 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117154 restraints weight = 2509.469| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.42 r_work: 0.3144 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2367 Z= 0.144 Angle : 0.548 7.053 3228 Z= 0.284 Chirality : 0.040 0.136 394 Planarity : 0.004 0.052 386 Dihedral : 5.458 51.667 313 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.32 % Allowed : 15.59 % Favored : 79.09 % 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 are not related in a simple way. whole: 1.91 (0.49), residues: 284 helix: 1.93 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.39 (0.86), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 198 PHE 0.013 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 2366) covalent geometry : angle 0.54775 / 0.28 ( 3226) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 0.02379 / 0.01 ( 2) hydrogen bonds : bond 0.04306 / 2.98 ( 179) hydrogen bonds : angle 4.23510 / 3.18 ( 537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: R 33 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7075 (ttp) REVERT: R 90 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8488 (mp) outliers start: 14 outliers final: 7 residues processed: 32 average time/residue: 0.2698 time to fit residues: 8.9276 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117924 restraints weight = 2583.717| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.43 r_work: 0.3148 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2367 Z= 0.143 Angle : 0.552 7.053 3228 Z= 0.286 Chirality : 0.040 0.134 394 Planarity : 0.004 0.053 386 Dihedral : 5.381 49.675 313 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.18 % Allowed : 15.97 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.50), residues: 284 helix: 1.94 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.39 (0.87), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 198 PHE 0.013 0.001 PHE R 113 TRP 0.006 0.001 TRP R 158 HIS 0.003 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2366) covalent geometry : angle 0.55208 / 0.29 ( 3226) SS BOND : bond 0.00271 / 0.14 ( 1) SS BOND : angle 0.01585 / 0.01 ( 2) hydrogen bonds : bond 0.04270 / 2.96 ( 179) hydrogen bonds : angle 4.23304 / 3.19 ( 537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: R 33 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7142 (ttp) REVERT: R 90 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8515 (mp) outliers start: 11 outliers final: 7 residues processed: 29 average time/residue: 0.2639 time to fit residues: 7.9073 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120011 restraints weight = 2601.661| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.44 r_work: 0.3165 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2367 Z= 0.122 Angle : 0.529 7.076 3228 Z= 0.272 Chirality : 0.039 0.125 394 Planarity : 0.004 0.052 386 Dihedral : 5.147 45.798 313 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.42 % Allowed : 16.73 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.50), residues: 284 helix: 2.06 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.37 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 264 TYR 0.007 0.001 TYR R 118 PHE 0.012 0.001 PHE R 113 TRP 0.005 0.001 TRP R 158 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 2366) covalent geometry : angle 0.52939 / 0.27 ( 3226) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 0.20998 / 0.12 ( 2) hydrogen bonds : bond 0.03904 / 2.71 ( 179) hydrogen bonds : angle 4.14493 / 3.11 ( 537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7916 (mp) cc_final: 0.7697 (mp) outliers start: 9 outliers final: 6 residues processed: 29 average time/residue: 0.3153 time to fit residues: 9.4571 Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119240 restraints weight = 2570.922| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.47 r_work: 0.3202 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2367 Z= 0.123 Angle : 0.536 7.068 3228 Z= 0.275 Chirality : 0.039 0.123 394 Planarity : 0.004 0.053 386 Dihedral : 5.129 45.522 313 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.42 % Allowed : 17.49 % Favored : 79.09 % 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 are not related in a simple way. whole: 2.28 (0.50), residues: 284 helix: 2.20 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.92 (0.82), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 118 PHE 0.012 0.001 PHE R 113 TRP 0.006 0.001 TRP R 158 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2366) covalent geometry : angle 0.53628 / 0.27 ( 3226) SS BOND : bond 0.00259 / 0.14 ( 1) SS BOND : angle 0.21419 / 0.12 ( 2) hydrogen bonds : bond 0.03927 / 2.73 ( 179) hydrogen bonds : angle 4.13953 / 3.11 ( 537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 865.01 seconds wall clock time: 15 minutes 26.48 seconds (926.48 seconds total)