Starting phenix.real_space_refine on Tue Aug 4 12:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxo_64588/08_2026/9uxo_64588.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.100 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 20 5.16 5 C 1555 2.51 5 N 376 2.21 5 O 405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 2356 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2344 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 12 Unusual residues: {'MAE': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 1.04, per 1000 atoms: 0.44 Number of scatterers: 2356 At special positions: 0 Unit cell: (54.12, 57.4, 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 20 16.00 O 405 8.00 N 376 7.00 C 1555 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 94.5 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 86.0% alpha, 1.4% 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 34 Processing helix chain 'R' and resid 34 through 60 removed outlier: 4.114A pdb=" N VAL R 38 " --> pdb=" O HIS R 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) 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 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.860A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.513A pdb=" N PHE R 170 " --> pdb=" O PRO R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.949A 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 303 removed outlier: 3.707A pdb=" N VAL R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 317 Processing sheet with id=AA1, first strand: chain 'R' and resid 174 through 176 185 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 704 1.35 - 1.46: 618 1.46 - 1.58: 1063 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 2411 Sorted by residual: bond pdb=" C1 MAE R 401 " pdb=" C2 MAE R 401 " ideal model delta sigma weight residual 1.513 1.476 0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C3 MAE R 401 " pdb=" C4 MAE R 401 " ideal model delta sigma weight residual 1.510 1.478 0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" CA LEU R 86 " pdb=" C LEU R 86 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.36e-01 bond pdb=" CB PHE R 104 " pdb=" CG PHE R 104 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 5.83e-01 bond pdb=" CA ILE R 166 " pdb=" C ILE R 166 " ideal model delta sigma weight residual 1.524 1.532 -0.007 1.05e-02 9.07e+03 4.95e-01 ... (remaining 2406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3232 1.77 - 3.54: 32 3.54 - 5.31: 17 5.31 - 7.08: 4 7.08 - 8.85: 2 Bond angle restraints: 3287 Sorted by residual: angle pdb=" O1 MAE R 401 " pdb=" C1 MAE R 401 " pdb=" O2 MAE R 401 " ideal model delta sigma weight residual 127.57 118.72 8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" N VAL R 46 " pdb=" CA VAL R 46 " pdb=" C VAL R 46 " ideal model delta sigma weight residual 112.96 110.21 2.75 1.00e+00 1.00e+00 7.59e+00 angle pdb=" C TYR R 58 " pdb=" N ILE R 59 " pdb=" CA ILE R 59 " ideal model delta sigma weight residual 123.08 120.47 2.61 1.01e+00 9.80e-01 6.68e+00 angle pdb=" O3 MAE R 401 " pdb=" C4 MAE R 401 " pdb=" O4 MAE R 401 " ideal model delta sigma weight residual 126.30 118.64 7.66 3.00e+00 1.11e-01 6.52e+00 angle pdb=" CA VAL R 46 " pdb=" C VAL R 46 " pdb=" O VAL R 46 " ideal model delta sigma weight residual 119.29 121.23 -1.94 8.40e-01 1.42e+00 5.35e+00 ... (remaining 3282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 1201 14.72 - 29.43: 151 29.43 - 44.15: 44 44.15 - 58.86: 15 58.86 - 73.58: 4 Dihedral angle restraints: 1415 sinusoidal: 541 harmonic: 874 Sorted by residual: dihedral pdb=" CB MET R 72 " pdb=" CG MET R 72 " pdb=" SD MET R 72 " pdb=" CE MET R 72 " ideal model delta sinusoidal sigma weight residual 60.00 119.35 -59.35 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET R 62 " pdb=" CG MET R 62 " pdb=" SD MET R 62 " pdb=" CE MET R 62 " ideal model delta sinusoidal sigma weight residual -60.00 -118.94 58.94 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS R 236 " pdb=" CB LYS R 236 " pdb=" CG LYS R 236 " pdb=" CD LYS R 236 " ideal model delta sinusoidal sigma weight residual 180.00 -121.72 -58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 215 0.022 - 0.043: 89 0.043 - 0.065: 66 0.065 - 0.087: 17 0.087 - 0.108: 16 Chirality restraints: 403 Sorted by residual: chirality pdb=" CA PRO R 87 " pdb=" N PRO R 87 " pdb=" C PRO R 87 " pdb=" CB PRO R 87 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.92e-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 2.41 0.10 2.00e-01 2.50e+01 2.70e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 400 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO R 210 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C PHE R 44 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE R 44 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU R 45 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 43 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ILE R 43 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 43 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE R 44 " -0.008 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 572 2.79 - 3.32: 2426 3.32 - 3.85: 4189 3.85 - 4.37: 4568 4.37 - 4.90: 8080 Nonbonded interactions: 19835 Sorted by model distance: nonbonded pdb=" NZ LYS R 32 " pdb=" OE2 GLU R 97 " model vdw 2.268 3.120 nonbonded pdb=" OD2 ASP R 185 " pdb=" OG1 THR R 187 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O HOH R 501 " model vdw 2.332 3.040 nonbonded pdb=" OD1 ASP R 185 " pdb=" OG SER R 188 " model vdw 2.338 3.040 nonbonded pdb=" O VAL R 53 " pdb=" OG SER R 56 " model vdw 2.349 3.040 ... (remaining 19830 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.003 0.037 2412 Z= 0.138 Angle : 0.612 8.851 3289 Z= 0.311 Chirality : 0.037 0.108 403 Planarity : 0.004 0.035 394 Dihedral : 15.660 73.578 842 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.37 % Allowed : 17.78 % Favored : 81.85 % 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: 1.80 (0.50), residues: 290 helix: 1.81 (0.35), residues: 234 sheet: None (None), residues: 0 loop : -1.50 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 127 TRP 0.012 0.001 TRP R 158 HIS 0.001 0.000 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 2411) covalent geometry : angle 0.61253 / 0.31 ( 3287) SS BOND : bond 0.00167 / 0.09 ( 1) SS BOND : angle 0.38613 / 0.22 ( 2) hydrogen bonds : bond 0.11453 / 8.03 ( 185) hydrogen bonds : angle 5.64727 / 4.11 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.079 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.2900 time to fit residues: 8.4585 Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.143891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109696 restraints weight = 2466.381| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.49 r_work: 0.3070 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2412 Z= 0.158 Angle : 0.539 5.647 3289 Z= 0.281 Chirality : 0.040 0.113 403 Planarity : 0.004 0.034 394 Dihedral : 5.748 55.177 319 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.70 % Allowed : 14.44 % Favored : 81.85 % 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: 2.24 (0.50), residues: 290 helix: 2.13 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -1.40 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.016 0.001 TYR R 82 PHE 0.015 0.002 PHE R 104 TRP 0.009 0.001 TRP R 158 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 2411) covalent geometry : angle 0.53894 / 0.28 ( 3287) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 0.31235 / 0.17 ( 2) hydrogen bonds : bond 0.04547 / 3.03 ( 185) hydrogen bonds : angle 4.20962 / 2.98 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.115 Fit side-chains REVERT: R 118 TYR cc_start: 0.8497 (m-80) cc_final: 0.8285 (m-80) outliers start: 10 outliers final: 4 residues processed: 33 average time/residue: 0.2814 time to fit residues: 9.7737 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.0020 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.146441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111834 restraints weight = 2414.487| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.47 r_work: 0.3085 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2412 Z= 0.130 Angle : 0.526 5.874 3289 Z= 0.271 Chirality : 0.038 0.109 403 Planarity : 0.004 0.031 394 Dihedral : 5.345 53.667 319 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.85 % Allowed : 16.30 % Favored : 81.85 % 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: 2.25 (0.50), residues: 290 helix: 2.14 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -1.44 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 113 TRP 0.009 0.002 TRP R 158 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 2411) covalent geometry : angle 0.52139 / 0.27 ( 3287) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 2.82237 / 1.53 ( 2) hydrogen bonds : bond 0.03951 / 2.65 ( 185) hydrogen bonds : angle 4.02432 / 2.85 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.051 Fit side-chains REVERT: R 118 TYR cc_start: 0.8475 (m-80) cc_final: 0.8245 (m-80) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.2386 time to fit residues: 8.5415 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111733 restraints weight = 2419.286| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.45 r_work: 0.3083 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2412 Z= 0.146 Angle : 0.571 7.109 3289 Z= 0.291 Chirality : 0.039 0.112 403 Planarity : 0.004 0.031 394 Dihedral : 5.342 54.136 319 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.96 % Allowed : 15.56 % Favored : 81.48 % 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: 2.17 (0.50), residues: 290 helix: 2.11 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -1.62 (0.75), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 261 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 113 TRP 0.008 0.002 TRP R 99 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 2411) covalent geometry : angle 0.56346 / 0.29 ( 3287) SS BOND : bond 0.00261 / 0.14 ( 1) SS BOND : angle 3.84749 / 2.15 ( 2) hydrogen bonds : bond 0.04011 / 2.68 ( 185) hydrogen bonds : angle 4.14655 / 2.88 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: R 118 TYR cc_start: 0.8499 (m-80) cc_final: 0.8240 (m-80) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.2644 time to fit residues: 8.8605 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111471 restraints weight = 2438.333| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.47 r_work: 0.3086 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2412 Z= 0.132 Angle : 0.542 5.915 3289 Z= 0.277 Chirality : 0.039 0.110 403 Planarity : 0.003 0.030 394 Dihedral : 5.046 53.285 318 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.96 % Allowed : 16.30 % Favored : 80.74 % 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: 2.17 (0.50), residues: 290 helix: 2.14 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -1.78 (0.74), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.015 0.001 TYR R 82 PHE 0.012 0.001 PHE R 113 TRP 0.008 0.001 TRP R 158 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 2411) covalent geometry : angle 0.53883 / 0.28 ( 3287) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 2.39209 / 1.36 ( 2) hydrogen bonds : bond 0.03887 / 2.58 ( 185) hydrogen bonds : angle 4.08969 / 2.86 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: R 118 TYR cc_start: 0.8512 (m-80) cc_final: 0.8310 (m-80) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.2367 time to fit residues: 8.2674 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111554 restraints weight = 2391.931| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.46 r_work: 0.3092 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2412 Z= 0.137 Angle : 0.569 6.826 3289 Z= 0.288 Chirality : 0.039 0.111 403 Planarity : 0.003 0.029 394 Dihedral : 5.084 53.492 318 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.33 % Allowed : 17.04 % Favored : 79.63 % 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: 2.11 (0.50), residues: 290 helix: 2.11 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -1.88 (0.74), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.015 0.001 TYR R 82 PHE 0.014 0.001 PHE R 113 TRP 0.008 0.002 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 2411) covalent geometry : angle 0.56464 / 0.29 ( 3287) SS BOND : bond 0.00248 / 0.13 ( 1) SS BOND : angle 2.86998 / 1.52 ( 2) hydrogen bonds : bond 0.03896 / 2.59 ( 185) hydrogen bonds : angle 4.10662 / 2.87 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.053 Fit side-chains REVERT: R 118 TYR cc_start: 0.8511 (m-80) cc_final: 0.8299 (m-80) outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 0.2350 time to fit residues: 7.9188 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110142 restraints weight = 2442.836| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.46 r_work: 0.3065 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2412 Z= 0.160 Angle : 0.583 6.332 3289 Z= 0.295 Chirality : 0.040 0.117 403 Planarity : 0.004 0.030 394 Dihedral : 5.093 53.720 318 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.70 % Allowed : 16.30 % Favored : 80.00 % 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: 2.00 (0.50), residues: 290 helix: 2.03 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -1.90 (0.75), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 261 TYR 0.015 0.001 TYR R 82 PHE 0.014 0.002 PHE R 113 TRP 0.007 0.002 TRP R 99 HIS 0.003 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 2411) covalent geometry : angle 0.57750 / 0.29 ( 3287) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 3.24622 / 1.73 ( 2) hydrogen bonds : bond 0.04175 / 2.79 ( 185) hydrogen bonds : angle 4.14073 / 2.90 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.051 Fit side-chains REVERT: R 39 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7175 (mp) outliers start: 10 outliers final: 5 residues processed: 33 average time/residue: 0.2121 time to fit residues: 7.3313 Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110967 restraints weight = 2395.689| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.46 r_work: 0.3081 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2412 Z= 0.139 Angle : 0.566 6.008 3289 Z= 0.286 Chirality : 0.039 0.119 403 Planarity : 0.004 0.030 394 Dihedral : 5.029 53.003 318 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.96 % Allowed : 17.41 % Favored : 79.63 % 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: 2.02 (0.50), residues: 290 helix: 2.00 (0.34), residues: 238 sheet: None (None), residues: 0 loop : -1.89 (0.78), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 113 TRP 0.009 0.002 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2411) covalent geometry : angle 0.56176 / 0.28 ( 3287) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 2.74366 / 1.46 ( 2) hydrogen bonds : bond 0.03953 / 2.63 ( 185) hydrogen bonds : angle 4.09664 / 2.88 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.057 Fit side-chains REVERT: R 39 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7136 (mp) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.1981 time to fit residues: 6.0142 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110603 restraints weight = 2452.079| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.47 r_work: 0.3071 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2412 Z= 0.145 Angle : 0.562 6.000 3289 Z= 0.284 Chirality : 0.040 0.119 403 Planarity : 0.003 0.030 394 Dihedral : 4.982 52.097 318 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.59 % Allowed : 17.41 % Favored : 80.00 % 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: 1.99 (0.50), residues: 290 helix: 1.98 (0.34), residues: 238 sheet: None (None), residues: 0 loop : -1.87 (0.79), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.015 0.001 TYR R 82 PHE 0.014 0.001 PHE R 113 TRP 0.008 0.002 TRP R 158 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 2411) covalent geometry : angle 0.55769 / 0.28 ( 3287) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 2.73040 / 1.46 ( 2) hydrogen bonds : bond 0.04017 / 2.68 ( 185) hydrogen bonds : angle 4.09649 / 2.88 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.060 Fit side-chains REVERT: R 39 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7163 (mp) outliers start: 7 outliers final: 5 residues processed: 29 average time/residue: 0.2074 time to fit residues: 6.2824 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112100 restraints weight = 2479.994| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.49 r_work: 0.3090 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2412 Z= 0.129 Angle : 0.555 6.540 3289 Z= 0.279 Chirality : 0.039 0.114 403 Planarity : 0.004 0.030 394 Dihedral : 4.907 51.159 318 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.59 % Allowed : 17.78 % Favored : 79.63 % 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: 2.07 (0.51), residues: 290 helix: 2.05 (0.34), residues: 238 sheet: None (None), residues: 0 loop : -1.94 (0.78), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 113 TRP 0.009 0.001 TRP R 158 HIS 0.003 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2411) covalent geometry : angle 0.55209 / 0.28 ( 3287) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 2.19975 / 1.18 ( 2) hydrogen bonds : bond 0.03781 / 2.52 ( 185) hydrogen bonds : angle 4.04040 / 2.85 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.058 Fit side-chains REVERT: R 39 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7191 (mp) outliers start: 7 outliers final: 3 residues processed: 31 average time/residue: 0.2155 time to fit residues: 7.0201 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.145391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111071 restraints weight = 2466.181| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.48 r_work: 0.3075 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2412 Z= 0.142 Angle : 0.564 6.769 3289 Z= 0.283 Chirality : 0.040 0.117 403 Planarity : 0.004 0.030 394 Dihedral : 4.911 51.294 318 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.85 % Allowed : 18.89 % Favored : 79.26 % 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: 1.98 (0.50), residues: 290 helix: 1.99 (0.34), residues: 238 sheet: None (None), residues: 0 loop : -2.00 (0.78), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 268 TYR 0.015 0.001 TYR R 82 PHE 0.014 0.001 PHE R 113 TRP 0.008 0.002 TRP R 158 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 2411) covalent geometry : angle 0.56040 / 0.28 ( 3287) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 2.47476 / 1.33 ( 2) hydrogen bonds : bond 0.03947 / 2.64 ( 185) hydrogen bonds : angle 4.07047 / 2.87 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 776.93 seconds wall clock time: 13 minutes 58.66 seconds (838.66 seconds total)