Starting phenix.real_space_refine on Tue Aug 4 12:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxq_64590/08_2026/9uxq_64590.map" } resolution = 2.89 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= 0.111 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 1530 2.51 5 N 370 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2309 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2297 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'AKG': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 0.88, per 1000 atoms: 0.38 Number of scatterers: 2309 At special positions: 0 Unit cell: (56.58, 55.76, 73.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 390 8.00 N 370 7.00 C 1530 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: 0.21 Conformation dependent library (CDL) restraints added in 95.3 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: 14 helices and 1 sheets defined 86.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 35 through 61 Proline residue: R 49 - end of helix Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.747A pdb=" N SER R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.538A pdb=" N LEU R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.608A pdb=" N ARG R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.579A pdb=" N HIS R 145 " --> pdb=" O PHE R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.720A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.852A pdb=" N TRP R 197 " --> pdb=" O ASN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 225 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 removed outlier: 3.798A pdb=" N ALA R 292 " --> pdb=" O ARG R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.521A 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 175 178 hydrogen bonds defined for protein. 522 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: 0.22 Time building geometry restraints manager: 0.28 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: 510 1.33 - 1.45: 515 1.45 - 1.57: 1316 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 2366 Sorted by residual: bond pdb=" C1 AKG R 401 " pdb=" O2 AKG R 401 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C ILE R 29 " pdb=" N PRO R 30 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.36e-02 5.41e+03 1.12e+01 bond pdb=" C5 AKG R 401 " pdb=" O4 AKG R 401 " ideal model delta sigma weight residual 1.249 1.307 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C4 AKG R 401 " pdb=" C5 AKG R 401 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C5 AKG R 401 " pdb=" O3 AKG R 401 " ideal model delta sigma weight residual 1.247 1.214 0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 2361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3098 1.18 - 2.36: 89 2.36 - 3.53: 20 3.53 - 4.71: 11 4.71 - 5.89: 8 Bond angle restraints: 3226 Sorted by residual: angle pdb=" CA ILE R 29 " pdb=" CB ILE R 29 " pdb=" CG2 ILE R 29 " ideal model delta sigma weight residual 110.50 114.04 -3.54 1.70e+00 3.46e-01 4.33e+00 angle pdb=" C CYS R 253 " pdb=" N PHE R 254 " pdb=" CA PHE R 254 " ideal model delta sigma weight residual 122.79 119.11 3.68 1.78e+00 3.16e-01 4.26e+00 angle pdb=" CB MET R 72 " pdb=" CG MET R 72 " pdb=" SD MET R 72 " ideal model delta sigma weight residual 112.70 118.59 -5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" N PRO R 30 " pdb=" CA PRO R 30 " pdb=" C PRO R 30 " ideal model delta sigma weight residual 113.53 111.03 2.50 1.39e+00 5.18e-01 3.23e+00 angle pdb=" CB LYS R 61 " pdb=" CG LYS R 61 " pdb=" CD LYS R 61 " ideal model delta sigma weight residual 111.30 115.37 -4.07 2.30e+00 1.89e-01 3.13e+00 ... (remaining 3221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 1171 16.09 - 32.18: 166 32.18 - 48.27: 41 48.27 - 64.36: 7 64.36 - 80.45: 2 Dihedral angle restraints: 1387 sinusoidal: 531 harmonic: 856 Sorted by residual: dihedral pdb=" CG ARG R 63 " pdb=" CD ARG R 63 " pdb=" NE ARG R 63 " pdb=" CZ ARG R 63 " ideal model delta sinusoidal sigma weight residual 180.00 137.23 42.77 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CG ARG R 264 " pdb=" CD ARG R 264 " pdb=" NE ARG R 264 " pdb=" CZ ARG R 264 " ideal model delta sinusoidal sigma weight residual 180.00 138.17 41.83 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CB LYS R 196 " pdb=" CG LYS R 196 " pdb=" CD LYS R 196 " pdb=" CE LYS R 196 " ideal model delta sinusoidal sigma weight residual 60.00 117.24 -57.24 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 215 0.025 - 0.050: 96 0.050 - 0.074: 55 0.074 - 0.099: 19 0.099 - 0.124: 10 Chirality restraints: 395 Sorted by residual: chirality pdb=" CB THR R 84 " pdb=" CA THR R 84 " pdb=" OG1 THR R 84 " pdb=" CG2 THR R 84 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE R 29 " pdb=" N ILE R 29 " pdb=" C ILE R 29 " pdb=" CB ILE R 29 " both_signs ideal model delta sigma weight residual False 2.43 2.31 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ARG R 63 " pdb=" N ARG R 63 " pdb=" C ARG R 63 " pdb=" CB ARG R 63 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 392 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 63 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO R 64 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 64 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 64 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 166 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO R 167 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO R 210 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " 0.015 5.00e-02 4.00e+02 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 522 2.78 - 3.31: 2271 3.31 - 3.84: 4135 3.84 - 4.37: 4611 4.37 - 4.90: 8085 Nonbonded interactions: 19624 Sorted by model distance: nonbonded pdb=" OH TYR R 40 " pdb=" O4 AKG R 401 " model vdw 2.247 3.040 nonbonded pdb=" O TYR R 58 " pdb=" NE1 TRP R 65 " model vdw 2.316 3.120 nonbonded pdb=" O LEU R 202 " pdb=" OG1 THR R 206 " model vdw 2.339 3.040 nonbonded pdb=" OD2 ASP R 185 " pdb=" OG1 THR R 187 " model vdw 2.382 3.040 nonbonded pdb=" O ILE R 166 " pdb=" OG1 THR R 169 " model vdw 2.395 3.040 ... (remaining 19619 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: 1.620 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.240 Find NCS groups from input model: 0.000 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.004 0.069 2367 Z= 0.194 Angle : 0.585 5.888 3228 Z= 0.294 Chirality : 0.040 0.124 395 Planarity : 0.004 0.032 385 Dihedral : 16.053 80.445 826 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.38 % Allowed : 21.67 % Favored : 77.95 % 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: 1.83 (0.52), residues: 284 helix: 1.95 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.45 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.010 0.001 PHE R 113 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 2366) covalent geometry : angle 0.58483 / 0.29 ( 3226) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.38511 / 0.21 ( 2) hydrogen bonds : bond 0.11467 / 8.09 ( 178) hydrogen bonds : angle 6.55502 / 5.01 ( 522) *********************** 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 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.086 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.3103 time to fit residues: 9.6911 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 ILE 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: 4.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 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 = 0.3639 r_free = 0.3639 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118934 restraints weight = 2462.869| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.36 r_work: 0.3121 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2367 Z= 0.131 Angle : 0.537 5.584 3228 Z= 0.278 Chirality : 0.040 0.119 395 Planarity : 0.004 0.036 385 Dihedral : 6.457 54.193 316 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.42 % Allowed : 16.73 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.51), residues: 284 helix: 2.18 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.50 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.010 0.001 TYR R 58 PHE 0.008 0.001 PHE R 207 TRP 0.007 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 2366) covalent geometry : angle 0.53753 / 0.28 ( 3226) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 0.35164 / 0.19 ( 2) hydrogen bonds : bond 0.04191 / 2.95 ( 178) hydrogen bonds : angle 4.52777 / 3.70 ( 522) *********************** 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 39 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.053 Fit side-chains REVERT: R 62 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8110 (mtp) outliers start: 9 outliers final: 4 residues processed: 36 average time/residue: 0.2702 time to fit residues: 10.1079 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 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 = 0.3610 r_free = 0.3610 target = 0.147605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116909 restraints weight = 2516.402| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.35 r_work: 0.3106 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2367 Z= 0.145 Angle : 0.549 6.959 3228 Z= 0.284 Chirality : 0.041 0.169 395 Planarity : 0.004 0.037 385 Dihedral : 6.313 51.422 316 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.56 % Allowed : 15.21 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.51), residues: 284 helix: 2.19 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.63 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 207 TRP 0.008 0.001 TRP R 158 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 2366) covalent geometry : angle 0.54961 / 0.28 ( 3226) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.27466 / 0.15 ( 2) hydrogen bonds : bond 0.04201 / 2.94 ( 178) hydrogen bonds : angle 4.35885 / 3.62 ( 522) *********************** 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 39 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.055 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 34 average time/residue: 0.3831 time to fit residues: 13.4315 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 307 ASP 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 20 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 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 = 0.3613 r_free = 0.3613 target = 0.147732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117144 restraints weight = 2487.906| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.33 r_work: 0.3057 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2367 Z= 0.141 Angle : 0.536 6.428 3228 Z= 0.277 Chirality : 0.041 0.136 395 Planarity : 0.004 0.041 385 Dihedral : 5.925 44.406 316 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.94 % Allowed : 15.21 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.51), residues: 284 helix: 2.18 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.74 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 207 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2366) covalent geometry : angle 0.53603 / 0.28 ( 3226) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.28556 / 0.16 ( 2) hydrogen bonds : bond 0.04125 / 2.89 ( 178) hydrogen bonds : angle 4.29333 / 3.57 ( 522) *********************** 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 : 0.064 Fit side-chains REVERT: R 62 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (mtp) outliers start: 13 outliers final: 5 residues processed: 36 average time/residue: 0.3181 time to fit residues: 11.8973 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 : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 224 THR 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 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.150353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121206 restraints weight = 2435.602| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.34 r_work: 0.3128 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2367 Z= 0.139 Angle : 0.534 6.302 3228 Z= 0.275 Chirality : 0.041 0.127 395 Planarity : 0.004 0.042 385 Dihedral : 5.529 41.706 314 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.32 % Allowed : 15.59 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.51), residues: 284 helix: 2.20 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.77 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 207 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 2366) covalent geometry : angle 0.53419 / 0.28 ( 3226) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.27795 / 0.15 ( 2) hydrogen bonds : bond 0.04098 / 2.87 ( 178) hydrogen bonds : angle 4.27920 / 3.57 ( 522) *********************** 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 39 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.057 Fit side-chains REVERT: R 62 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8352 (mtp) REVERT: R 311 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7602 (mm-40) outliers start: 14 outliers final: 5 residues processed: 34 average time/residue: 0.2965 time to fit residues: 10.4059 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.148500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117990 restraints weight = 2447.485| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.33 r_work: 0.3060 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2367 Z= 0.141 Angle : 0.537 6.258 3228 Z= 0.276 Chirality : 0.041 0.122 395 Planarity : 0.004 0.045 385 Dihedral : 5.459 40.536 314 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.32 % Allowed : 15.59 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.51), residues: 284 helix: 2.21 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.78 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 207 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 2366) covalent geometry : angle 0.53745 / 0.28 ( 3226) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.27447 / 0.15 ( 2) hydrogen bonds : bond 0.04115 / 2.88 ( 178) hydrogen bonds : angle 4.27557 / 3.56 ( 522) *********************** 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 38 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.053 Fit side-chains REVERT: R 62 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: R 311 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7700 (mm-40) outliers start: 14 outliers final: 6 residues processed: 33 average time/residue: 0.2736 time to fit residues: 9.3817 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 1 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 = 0.3624 r_free = 0.3624 target = 0.148519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118184 restraints weight = 2471.738| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.33 r_work: 0.3119 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2367 Z= 0.144 Angle : 0.556 7.558 3228 Z= 0.287 Chirality : 0.042 0.201 395 Planarity : 0.005 0.046 385 Dihedral : 5.419 39.822 314 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.94 % Allowed : 17.11 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.51), residues: 284 helix: 2.20 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.79 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 241 TYR 0.008 0.001 TYR R 35 PHE 0.009 0.001 PHE R 207 TRP 0.009 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 2366) covalent geometry : angle 0.55639 / 0.29 ( 3226) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.28182 / 0.15 ( 2) hydrogen bonds : bond 0.04132 / 2.90 ( 178) hydrogen bonds : angle 4.28587 / 3.58 ( 522) *********************** 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 39 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.058 Fit side-chains REVERT: R 311 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7629 (mm-40) outliers start: 13 outliers final: 6 residues processed: 34 average time/residue: 0.2772 time to fit residues: 9.7674 Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118859 restraints weight = 2437.383| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.34 r_work: 0.3077 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2367 Z= 0.137 Angle : 0.551 7.374 3228 Z= 0.283 Chirality : 0.041 0.193 395 Planarity : 0.005 0.046 385 Dihedral : 5.341 38.441 314 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.42 % Allowed : 17.87 % Favored : 78.71 % 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 (0.51), residues: 284 helix: 2.22 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.77 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 113 TRP 0.009 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2366) covalent geometry : angle 0.55093 / 0.28 ( 3226) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.28525 / 0.16 ( 2) hydrogen bonds : bond 0.04036 / 2.83 ( 178) hydrogen bonds : angle 4.25920 / 3.56 ( 522) *********************** 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 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.083 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.2570 time to fit residues: 8.3243 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 : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.150220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121233 restraints weight = 2498.207| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.38 r_work: 0.3104 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2367 Z= 0.118 Angle : 0.533 7.399 3228 Z= 0.273 Chirality : 0.040 0.184 395 Planarity : 0.004 0.046 385 Dihedral : 5.108 34.850 314 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.66 % Allowed : 17.87 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.51), residues: 284 helix: 2.34 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.71 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 241 TYR 0.007 0.001 TYR R 118 PHE 0.008 0.001 PHE R 113 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 2366) covalent geometry : angle 0.53356 / 0.27 ( 3226) SS BOND : bond 0.00000 / 0.00 ( 1) SS BOND : angle 0.37320 / 0.20 ( 2) hydrogen bonds : bond 0.03780 / 2.67 ( 178) hydrogen bonds : angle 4.20291 / 3.52 ( 522) *********************** 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 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.050 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 29 average time/residue: 0.1944 time to fit residues: 5.8911 Evaluate side-chains 27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.151789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121959 restraints weight = 2519.742| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.37 r_work: 0.3114 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2367 Z= 0.141 Angle : 0.553 7.359 3228 Z= 0.284 Chirality : 0.042 0.183 395 Planarity : 0.004 0.046 385 Dihedral : 5.217 37.166 314 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.28 % Allowed : 18.63 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.51), residues: 284 helix: 2.27 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.75 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 241 TYR 0.008 0.001 TYR R 118 PHE 0.009 0.001 PHE R 113 TRP 0.008 0.001 TRP R 197 HIS 0.002 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2366) covalent geometry : angle 0.55327 / 0.28 ( 3226) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.28939 / 0.16 ( 2) hydrogen bonds : bond 0.04061 / 2.85 ( 178) hydrogen bonds : angle 4.24954 / 3.56 ( 522) ********************** 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 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.085 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.2683 time to fit residues: 7.8269 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 195 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121002 restraints weight = 2494.568| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.34 r_work: 0.3087 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2367 Z= 0.119 Angle : 0.534 7.336 3228 Z= 0.273 Chirality : 0.040 0.178 395 Planarity : 0.004 0.046 385 Dihedral : 5.043 34.524 314 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.66 % Allowed : 18.63 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.51), residues: 284 helix: 2.38 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.67 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 241 TYR 0.007 0.001 TYR R 118 PHE 0.008 0.001 PHE R 113 TRP 0.008 0.001 TRP R 197 HIS 0.001 0.001 HIS R 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 2366) covalent geometry : angle 0.53371 / 0.27 ( 3226) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.36369 / 0.20 ( 2) hydrogen bonds : bond 0.03794 / 2.69 ( 178) hydrogen bonds : angle 4.19650 / 3.52 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 833.38 seconds wall clock time: 14 minutes 57.41 seconds (897.41 seconds total)