Starting phenix.real_space_refine on Tue Aug 4 12:06:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.map" model { file = "/net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxn_64587/08_2026/9uxn_64587.cif" } resolution = 2.7 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= 0.003 sd= 0.119 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 1527 2.51 5 N 369 2.21 5 O 391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2306 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2295 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 11 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Time building chain proxies: 0.85, per 1000 atoms: 0.37 Number of scatterers: 2306 At special positions: 0 Unit cell: (55.48, 54.02, 75.19, 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 369 7.00 C 1527 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=2.25 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: 0.22 Conformation dependent library (CDL) restraints added in 82.4 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: 12 helices and 1 sheets defined 86.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 28 through 60 removed outlier: 4.119A 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 Processing helix chain 'R' and resid 66 through 95 Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.508A pdb=" N HIS R 145 " --> pdb=" O PHE R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.707A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 191 through 207 Processing helix chain 'R' and resid 207 through 228 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 303 removed outlier: 3.693A pdb=" N VAL R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 313 Processing sheet with id=AA1, first strand: chain 'R' and resid 174 through 175 183 hydrogen bonds defined for protein. 540 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: 0.24 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 384 1.33 - 1.45: 635 1.45 - 1.57: 1318 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 2362 Sorted by residual: bond pdb=" C ARG R 288 " pdb=" O ARG R 288 " ideal model delta sigma weight residual 1.244 1.206 0.038 1.00e-02 1.00e+04 1.44e+01 bond pdb=" CA ARG R 288 " pdb=" C ARG R 288 " ideal model delta sigma weight residual 1.520 1.544 -0.024 1.23e-02 6.61e+03 3.80e+00 bond pdb=" C SER R 287 " pdb=" N ARG R 288 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.50e-02 4.44e+03 3.58e+00 bond pdb=" C ARG R 288 " pdb=" N PRO R 289 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.05e+00 bond pdb=" C3 SIN R 401 " pdb=" C4 SIN R 401 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 2357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 3122 1.44 - 2.87: 72 2.87 - 4.31: 9 4.31 - 5.75: 13 5.75 - 7.19: 4 Bond angle restraints: 3220 Sorted by residual: angle pdb=" C ARG R 288 " pdb=" N PRO R 289 " pdb=" CA PRO R 289 " ideal model delta sigma weight residual 119.56 116.64 2.92 1.02e+00 9.61e-01 8.18e+00 angle pdb=" C ASN R 28 " pdb=" N ILE R 29 " pdb=" CA ILE R 29 " ideal model delta sigma weight residual 120.33 122.54 -2.21 8.00e-01 1.56e+00 7.65e+00 angle pdb=" C2 SIN R 401 " pdb=" C3 SIN R 401 " pdb=" C4 SIN R 401 " ideal model delta sigma weight residual 116.29 109.10 7.19 3.00e+00 1.11e-01 5.74e+00 angle pdb=" C CYS R 253 " pdb=" N PHE R 254 " pdb=" CA PHE R 254 " ideal model delta sigma weight residual 122.79 118.60 4.19 1.78e+00 3.16e-01 5.53e+00 angle pdb=" O3 SIN R 401 " pdb=" C4 SIN R 401 " pdb=" O4 SIN R 401 " ideal model delta sigma weight residual 125.74 118.97 6.77 3.00e+00 1.11e-01 5.09e+00 ... (remaining 3215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1218 16.94 - 33.89: 131 33.89 - 50.83: 30 50.83 - 67.78: 6 67.78 - 84.72: 2 Dihedral angle restraints: 1387 sinusoidal: 531 harmonic: 856 Sorted by residual: dihedral pdb=" CG ARG R 180 " pdb=" CD ARG R 180 " pdb=" NE ARG R 180 " pdb=" CZ ARG R 180 " ideal model delta sinusoidal sigma weight residual -90.00 -133.12 43.12 2 1.50e+01 4.44e-03 9.97e+00 dihedral pdb=" CB GLU R 97 " pdb=" CG GLU R 97 " pdb=" CD GLU R 97 " pdb=" OE1 GLU R 97 " ideal model delta sinusoidal sigma weight residual 0.00 84.72 -84.72 1 3.00e+01 1.11e-03 9.69e+00 dihedral pdb=" CA LEU R 192 " pdb=" CB LEU R 192 " pdb=" CG LEU R 192 " pdb=" CD1 LEU R 192 " ideal model delta sinusoidal sigma weight residual 180.00 124.91 55.09 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 1384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 246 0.032 - 0.064: 103 0.064 - 0.096: 31 0.096 - 0.128: 12 0.128 - 0.160: 2 Chirality restraints: 394 Sorted by residual: chirality pdb=" CA ARG R 288 " pdb=" N ARG R 288 " pdb=" C ARG R 288 " pdb=" CB ARG R 288 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA MET R 139 " pdb=" N MET R 139 " pdb=" C MET R 139 " pdb=" CB MET R 139 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CG LEU R 192 " pdb=" CB LEU R 192 " pdb=" CD1 LEU R 192 " pdb=" CD2 LEU R 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 391 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 166 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO R 167 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 288 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C ARG R 288 " -0.022 2.00e-02 2.50e+03 pdb=" O ARG R 288 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO R 289 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO R 210 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " 0.017 5.00e-02 4.00e+02 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 575 2.80 - 3.33: 2385 3.33 - 3.85: 4159 3.85 - 4.38: 4565 4.38 - 4.90: 7927 Nonbonded interactions: 19611 Sorted by model distance: nonbonded pdb=" OH TYR R 284 " pdb=" O HOH R 501 " model vdw 2.276 3.040 nonbonded pdb=" NZ LYS R 32 " pdb=" OE2 GLU R 97 " model vdw 2.307 3.120 nonbonded pdb=" O TRP R 99 " pdb=" OG SER R 181 " model vdw 2.333 3.040 nonbonded pdb=" OH TYR R 118 " pdb=" NH2 ARG R 261 " model vdw 2.361 3.120 nonbonded pdb=" O THR R 231 " pdb=" NE2 GLN R 237 " model vdw 2.372 3.120 ... (remaining 19606 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: 1.320 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.210 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.006 0.221 2363 Z= 0.296 Angle : 0.651 7.843 3222 Z= 0.333 Chirality : 0.041 0.160 394 Planarity : 0.004 0.040 384 Dihedral : 15.223 84.721 826 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.76 % Allowed : 14.12 % Favored : 85.11 % 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: 2.34 (0.49), residues: 284 helix: 2.23 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.13 (0.72), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 288 TYR 0.010 0.001 TYR R 82 PHE 0.017 0.002 PHE R 170 TRP 0.008 0.001 TRP R 158 HIS 0.005 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 ( 2362) covalent geometry : angle 0.63622 / 0.33 ( 3220) SS BOND : bond 0.22070 / 11.62 ( 1) SS BOND : angle 5.62674 / 2.97 ( 2) hydrogen bonds : bond 0.12009 / 7.21 ( 183) hydrogen bonds : angle 6.02267 / 4.56 ( 540) *********************** 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 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.054 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.2634 time to fit residues: 7.7321 Evaluate side-chains 25 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 185 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.156221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122225 restraints weight = 2465.427| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.59 r_work: 0.3336 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2363 Z= 0.157 Angle : 0.555 5.122 3222 Z= 0.290 Chirality : 0.040 0.122 394 Planarity : 0.004 0.043 384 Dihedral : 7.700 59.234 319 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.05 % Allowed : 13.74 % Favored : 83.21 % 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: 2.69 (0.49), residues: 284 helix: 2.49 (0.33), residues: 226 sheet: None (None), residues: 0 loop : -1.20 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 261 TYR 0.015 0.001 TYR R 118 PHE 0.011 0.002 PHE R 113 TRP 0.008 0.001 TRP R 158 HIS 0.005 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 2362) covalent geometry : angle 0.55504 / 0.29 ( 3220) SS BOND : bond 0.00645 / 0.34 ( 1) SS BOND : angle 0.11248 / 0.06 ( 2) hydrogen bonds : bond 0.04969 / 3.39 ( 183) hydrogen bonds : angle 4.37168 / 3.32 ( 540) *********************** 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 36 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.088 Fit side-chains REVERT: R 235 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7237 (tt) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.3574 time to fit residues: 11.8518 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120999 restraints weight = 2545.020| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.60 r_work: 0.3318 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2363 Z= 0.166 Angle : 0.558 5.104 3222 Z= 0.291 Chirality : 0.041 0.123 394 Planarity : 0.005 0.045 384 Dihedral : 6.839 57.030 315 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.58 % Allowed : 14.50 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.48), residues: 284 helix: 2.37 (0.33), residues: 226 sheet: None (None), residues: 0 loop : -1.24 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 241 TYR 0.014 0.001 TYR R 118 PHE 0.013 0.002 PHE R 170 TRP 0.009 0.001 TRP R 158 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 2362) covalent geometry : angle 0.55798 / 0.29 ( 3220) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.07948 / 0.05 ( 2) hydrogen bonds : bond 0.05033 / 3.44 ( 183) hydrogen bonds : angle 4.29324 / 3.25 ( 540) *********************** 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 36 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.053 Fit side-chains REVERT: R 235 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7298 (tt) outliers start: 12 outliers final: 5 residues processed: 33 average time/residue: 0.2752 time to fit residues: 9.4407 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123002 restraints weight = 2524.047| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.63 r_work: 0.3337 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2363 Z= 0.138 Angle : 0.534 5.088 3222 Z= 0.275 Chirality : 0.039 0.119 394 Planarity : 0.004 0.044 384 Dihedral : 6.494 52.210 315 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.96 % Allowed : 14.12 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.49), residues: 284 helix: 2.44 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.23 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 240 TYR 0.012 0.001 TYR R 118 PHE 0.012 0.001 PHE R 170 TRP 0.008 0.001 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 2362) covalent geometry : angle 0.53452 / 0.28 ( 3220) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.22009 / 0.13 ( 2) hydrogen bonds : bond 0.04545 / 3.14 ( 183) hydrogen bonds : angle 4.20399 / 3.19 ( 540) *********************** 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 40 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.100 Fit side-chains REVERT: R 235 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7226 (tt) REVERT: R 248 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6670 (tp) outliers start: 13 outliers final: 5 residues processed: 37 average time/residue: 0.3243 time to fit residues: 12.4082 Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 28 ASN R 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.158140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124980 restraints weight = 2510.402| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.61 r_work: 0.3321 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2363 Z= 0.124 Angle : 0.519 5.055 3222 Z= 0.266 Chirality : 0.039 0.118 394 Planarity : 0.004 0.042 384 Dihedral : 6.034 46.634 315 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.96 % Allowed : 15.65 % Favored : 79.39 % 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: 2.72 (0.49), residues: 284 helix: 2.52 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.21 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.011 0.001 TYR R 118 PHE 0.012 0.001 PHE R 113 TRP 0.007 0.001 TRP R 158 HIS 0.002 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2362) covalent geometry : angle 0.51918 / 0.27 ( 3220) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 0.31043 / 0.18 ( 2) hydrogen bonds : bond 0.04223 / 2.94 ( 183) hydrogen bonds : angle 4.14357 / 3.15 ( 540) *********************** 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 37 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7172 (tt) outliers start: 13 outliers final: 5 residues processed: 34 average time/residue: 0.2041 time to fit residues: 7.3893 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.157203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124176 restraints weight = 2503.409| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.60 r_work: 0.3330 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2363 Z= 0.136 Angle : 0.540 5.801 3222 Z= 0.276 Chirality : 0.039 0.131 394 Planarity : 0.004 0.042 384 Dihedral : 5.955 45.664 315 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 16.41 % Favored : 79.39 % 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: 2.64 (0.49), residues: 284 helix: 2.47 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.24 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 241 TYR 0.012 0.001 TYR R 118 PHE 0.014 0.001 PHE R 170 TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 2362) covalent geometry : angle 0.53985 / 0.28 ( 3220) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.18235 / 0.10 ( 2) hydrogen bonds : bond 0.04392 / 3.05 ( 183) hydrogen bonds : angle 4.14510 / 3.14 ( 540) *********************** 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 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 revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7205 (tt) REVERT: R 248 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6684 (tp) outliers start: 11 outliers final: 7 residues processed: 31 average time/residue: 0.2816 time to fit residues: 9.1544 Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.156934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123624 restraints weight = 2526.639| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.65 r_work: 0.3314 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2363 Z= 0.136 Angle : 0.547 7.119 3222 Z= 0.276 Chirality : 0.039 0.120 394 Planarity : 0.004 0.041 384 Dihedral : 5.817 43.150 315 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.58 % Allowed : 16.41 % Favored : 79.01 % 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: 2.55 (0.49), residues: 284 helix: 2.42 (0.33), residues: 226 sheet: None (None), residues: 0 loop : -1.40 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 240 TYR 0.012 0.001 TYR R 118 PHE 0.014 0.001 PHE R 113 TRP 0.008 0.001 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 2362) covalent geometry : angle 0.54724 / 0.28 ( 3220) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.15017 / 0.08 ( 2) hydrogen bonds : bond 0.04415 / 3.09 ( 183) hydrogen bonds : angle 4.15504 / 3.14 ( 540) *********************** 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 35 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7186 (tt) REVERT: R 248 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6662 (tp) outliers start: 12 outliers final: 7 residues processed: 32 average time/residue: 0.1772 time to fit residues: 6.0183 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 : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.158136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124902 restraints weight = 2462.041| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.62 r_work: 0.3333 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2363 Z= 0.124 Angle : 0.537 7.470 3222 Z= 0.268 Chirality : 0.038 0.118 394 Planarity : 0.004 0.041 384 Dihedral : 5.515 38.911 315 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 16.79 % Favored : 79.01 % 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: 2.58 (0.50), residues: 284 helix: 2.45 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.41 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.011 0.001 TYR R 82 PHE 0.013 0.001 PHE R 170 TRP 0.007 0.001 TRP R 158 HIS 0.002 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 2362) covalent geometry : angle 0.53751 / 0.27 ( 3220) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.26913 / 0.15 ( 2) hydrogen bonds : bond 0.04191 / 2.93 ( 183) hydrogen bonds : angle 4.12442 / 3.13 ( 540) *********************** 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 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7146 (tt) REVERT: R 248 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6687 (tp) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.1419 time to fit residues: 4.9677 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 28 ASN Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.2626 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.161819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128358 restraints weight = 2501.363| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.63 r_work: 0.3392 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2363 Z= 0.114 Angle : 0.532 9.025 3222 Z= 0.264 Chirality : 0.038 0.132 394 Planarity : 0.004 0.040 384 Dihedral : 5.234 33.580 315 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 18.32 % Favored : 79.01 % 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: 2.63 (0.50), residues: 284 helix: 2.54 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.54 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 288 TYR 0.013 0.001 TYR R 40 PHE 0.016 0.001 PHE R 170 TRP 0.006 0.001 TRP R 158 HIS 0.001 0.000 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 2362) covalent geometry : angle 0.53221 / 0.26 ( 3220) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.56050 / 0.32 ( 2) hydrogen bonds : bond 0.03799 / 2.69 ( 183) hydrogen bonds : angle 4.10292 / 3.14 ( 540) *********************** 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: 7 poor density : 26 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7031 (tt) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.2169 time to fit residues: 7.2821 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126781 restraints weight = 2533.703| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.67 r_work: 0.3389 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2363 Z= 0.123 Angle : 0.552 8.652 3222 Z= 0.271 Chirality : 0.039 0.143 394 Planarity : 0.004 0.040 384 Dihedral : 5.241 33.868 315 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 18.70 % Favored : 78.63 % 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: 2.58 (0.50), residues: 284 helix: 2.50 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.54 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 268 TYR 0.010 0.001 TYR R 82 PHE 0.015 0.001 PHE R 170 TRP 0.006 0.001 TRP R 158 HIS 0.002 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 2362) covalent geometry : angle 0.55253 / 0.27 ( 3220) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.35964 / 0.20 ( 2) hydrogen bonds : bond 0.03982 / 2.82 ( 183) hydrogen bonds : angle 4.08783 / 3.12 ( 540) ********************** 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: 7 poor density : 24 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: R 235 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7111 (tt) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.2788 time to fit residues: 8.4734 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124789 restraints weight = 2483.750| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.62 r_work: 0.3326 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2363 Z= 0.138 Angle : 0.567 8.435 3222 Z= 0.280 Chirality : 0.039 0.153 394 Planarity : 0.004 0.040 384 Dihedral : 5.302 34.371 315 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.82 % Allowed : 17.56 % Favored : 78.63 % 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: 2.49 (0.50), residues: 284 helix: 2.44 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.59 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 268 TYR 0.013 0.002 TYR R 118 PHE 0.015 0.002 PHE R 170 TRP 0.008 0.001 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 2362) covalent geometry : angle 0.56705 / 0.28 ( 3220) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.14266 / 0.08 ( 2) hydrogen bonds : bond 0.04315 / 3.06 ( 183) hydrogen bonds : angle 4.14359 / 3.16 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 889.06 seconds wall clock time: 15 minutes 53.71 seconds (953.71 seconds total)