Starting phenix.real_space_refine on Fri Sep 11 11:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.cif Found real_map, /net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10db_75081/09_2026/10db_75081.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 3 5.16 5 C 5598 2.51 5 N 1461 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8817 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2939 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 376} Chain breaks: 1 Chain: "A" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2939 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2939 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 376} Chain breaks: 1 Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8817 At special positions: 0 Unit cell: (107, 110.21, 73.83, 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 3 16.00 O 1755 8.00 N 1461 7.00 C 5598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.91 Conformation dependent library (CDL) restraints added in 324.4 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 2.7% alpha, 55.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.638A pdb=" N ILE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'A' and resid 25 through 29 removed outlier: 3.578A pdb=" N ILE A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 29' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.594A pdb=" N ILE C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 29' Processing helix chain 'C' and resid 312 through 316 Processing sheet with id=AA1, first strand: chain 'B' and resid 210 through 212 removed outlier: 3.547A pdb=" N GLY B 272 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY B 45 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS B 61 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B 81 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 114 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 83 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 112 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 85 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ARG B 110 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN B 131 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL B 145 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE B 169 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B 147 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.538A pdb=" N GLY A 272 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 45 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS A 61 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 81 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 114 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE A 83 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 112 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN A 85 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 12.108A pdb=" N ARG A 110 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN A 131 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL A 145 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE A 169 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A 147 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA5, first strand: chain 'C' and resid 210 through 211 removed outlier: 7.073A pdb=" N GLY C 45 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS C 61 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS C 81 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU C 114 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE C 83 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 112 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN C 85 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ARG C 110 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN C 131 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 145 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE C 169 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 147 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 301 through 302 558 hydrogen bonds defined for protein. 1518 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: 1.31 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2928 1.34 - 1.46: 1844 1.46 - 1.57: 4225 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 9003 Sorted by residual: bond pdb=" N GLY A 257 " pdb=" CA GLY A 257 " ideal model delta sigma weight residual 1.452 1.444 0.009 1.03e-02 9.43e+03 7.39e-01 bond pdb=" CA PHE C 244 " pdb=" C PHE C 244 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 6.96e-01 bond pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 6.61e-01 bond pdb=" C GLY A 128 " pdb=" O GLY A 128 " ideal model delta sigma weight residual 1.236 1.229 0.008 1.02e-02 9.61e+03 5.64e-01 bond pdb=" N GLY B 257 " pdb=" CA GLY B 257 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.06e-02 8.90e+03 5.59e-01 ... (remaining 8998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 11317 0.78 - 1.56: 798 1.56 - 2.35: 74 2.35 - 3.13: 22 3.13 - 3.91: 8 Bond angle restraints: 12219 Sorted by residual: angle pdb=" N ASN B 102 " pdb=" CA ASN B 102 " pdb=" C ASN B 102 " ideal model delta sigma weight residual 110.88 107.88 3.00 1.28e+00 6.10e-01 5.51e+00 angle pdb=" N ASN A 102 " pdb=" CA ASN A 102 " pdb=" C ASN A 102 " ideal model delta sigma weight residual 110.61 107.90 2.71 1.25e+00 6.40e-01 4.71e+00 angle pdb=" N ASN C 102 " pdb=" CA ASN C 102 " pdb=" C ASN C 102 " ideal model delta sigma weight residual 110.61 108.02 2.59 1.25e+00 6.40e-01 4.28e+00 angle pdb=" N GLY C 246 " pdb=" CA GLY C 246 " pdb=" C GLY C 246 " ideal model delta sigma weight residual 113.18 116.63 -3.45 2.37e+00 1.78e-01 2.12e+00 angle pdb=" N GLY B 246 " pdb=" CA GLY B 246 " pdb=" C GLY B 246 " ideal model delta sigma weight residual 113.18 116.48 -3.30 2.37e+00 1.78e-01 1.94e+00 ... (remaining 12214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 4956 16.28 - 32.55: 120 32.55 - 48.83: 33 48.83 - 65.11: 8 65.11 - 81.38: 4 Dihedral angle restraints: 5121 sinusoidal: 1878 harmonic: 3243 Sorted by residual: dihedral pdb=" CA ILE A 247 " pdb=" CB ILE A 247 " pdb=" CG1 ILE A 247 " pdb=" CD1 ILE A 247 " ideal model delta sinusoidal sigma weight residual 60.00 113.07 -53.07 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA LEU B 274 " pdb=" CB LEU B 274 " pdb=" CG LEU B 274 " pdb=" CD1 LEU B 274 " ideal model delta sinusoidal sigma weight residual 180.00 132.99 47.01 3 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CA LEU C 274 " pdb=" CB LEU C 274 " pdb=" CG LEU C 274 " pdb=" CD1 LEU C 274 " ideal model delta sinusoidal sigma weight residual 180.00 134.73 45.27 3 1.50e+01 4.44e-03 8.14e+00 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 699 0.025 - 0.050: 393 0.050 - 0.075: 128 0.075 - 0.100: 45 0.100 - 0.126: 52 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 337 " pdb=" N ILE A 337 " pdb=" C ILE A 337 " pdb=" CB ILE A 337 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL A 235 " pdb=" N VAL A 235 " pdb=" C VAL A 235 " pdb=" CB VAL A 235 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 1314 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 387 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO B 388 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 387 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 388 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 387 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 388 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.021 5.00e-02 4.00e+02 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1546 2.77 - 3.30: 7168 3.30 - 3.84: 13618 3.84 - 4.37: 16096 4.37 - 4.90: 30604 Nonbonded interactions: 69032 Sorted by model distance: nonbonded pdb=" OG SER B 289 " pdb=" OG1 THR B 342 " model vdw 2.240 3.040 nonbonded pdb=" OG SER C 289 " pdb=" OG1 THR C 342 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 289 " pdb=" OG1 THR A 342 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU A 319 " pdb=" NH2 ARG A 381 " model vdw 2.363 3.120 nonbonded pdb=" OE2 GLU B 319 " pdb=" NH2 ARG B 381 " model vdw 2.373 3.120 ... (remaining 69027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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: 2.670 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 0.015 9003 Z= 0.138 Angle : 0.434 3.910 12219 Z= 0.258 Chirality : 0.040 0.126 1317 Planarity : 0.002 0.038 1611 Dihedral : 8.853 81.382 3087 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.78 % Allowed : 3.88 % Favored : 95.35 % 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: 0.69 (0.25), residues: 1131 helix: -4.11 (0.88), residues: 18 sheet: 1.49 (0.20), residues: 681 loop : -1.12 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 335 TYR 0.011 0.001 TYR C 113 PHE 0.012 0.001 PHE B 395 TRP 0.007 0.001 TRP B 249 HIS 0.001 0.000 HIS C 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 9003) covalent geometry : angle 0.43389 / 0.26 (12219) hydrogen bonds : bond 0.17891 / 11.20 ( 558) hydrogen bonds : angle 7.46162 / 5.08 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.212 Fit side-chains REVERT: B 423 LYS cc_start: 0.8465 (mttt) cc_final: 0.8198 (mttp) outliers start: 7 outliers final: 3 residues processed: 96 average time/residue: 0.5979 time to fit residues: 60.9829 Evaluate side-chains 37 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 142 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.093301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.065493 restraints weight = 13564.926| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.09 r_work: 0.2656 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9003 Z= 0.127 Angle : 0.490 3.958 12219 Z= 0.285 Chirality : 0.042 0.133 1317 Planarity : 0.003 0.038 1611 Dihedral : 4.397 57.729 1245 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.44 % Allowed : 9.97 % Favored : 88.59 % 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: 0.95 (0.25), residues: 1131 helix: -3.87 (1.00), residues: 18 sheet: 1.64 (0.20), residues: 672 loop : -0.86 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.011 0.001 TYR C 113 PHE 0.017 0.001 PHE B 395 TRP 0.006 0.001 TRP C 286 HIS 0.002 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9003) covalent geometry : angle 0.49005 / 0.29 (12219) hydrogen bonds : bond 0.03812 / 2.49 ( 558) hydrogen bonds : angle 4.96523 / 3.39 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.418 Fit side-chains REVERT: C 27 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8445 (mt-10) outliers start: 13 outliers final: 3 residues processed: 51 average time/residue: 0.4037 time to fit residues: 22.9500 Evaluate side-chains 32 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 157 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.065776 restraints weight = 13468.227| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.11 r_work: 0.2660 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9003 Z= 0.111 Angle : 0.461 3.786 12219 Z= 0.269 Chirality : 0.042 0.135 1317 Planarity : 0.003 0.038 1611 Dihedral : 3.722 18.954 1239 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.11 % Allowed : 9.86 % Favored : 89.04 % 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: 0.95 (0.25), residues: 1131 helix: -3.75 (1.05), residues: 18 sheet: 1.55 (0.20), residues: 681 loop : -0.75 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.011 0.001 TYR A 113 PHE 0.017 0.001 PHE B 395 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9003) covalent geometry : angle 0.46087 / 0.27 (12219) hydrogen bonds : bond 0.03300 / 2.15 ( 558) hydrogen bonds : angle 4.65667 / 3.18 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.335 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 39 average time/residue: 0.3970 time to fit residues: 17.2884 Evaluate side-chains 32 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.090764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.062747 restraints weight = 13841.539| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.14 r_work: 0.2605 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 9003 Z= 0.219 Angle : 0.520 4.313 12219 Z= 0.298 Chirality : 0.043 0.136 1317 Planarity : 0.003 0.037 1611 Dihedral : 4.071 19.724 1239 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 10.08 % Favored : 88.15 % 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: 0.77 (0.25), residues: 1131 helix: -3.88 (1.02), residues: 18 sheet: 1.45 (0.20), residues: 672 loop : -0.84 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 417 TYR 0.015 0.001 TYR C 113 PHE 0.021 0.002 PHE B 395 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 9003) covalent geometry : angle 0.52033 / 0.30 (12219) hydrogen bonds : bond 0.03754 / 2.44 ( 558) hydrogen bonds : angle 4.74075 / 3.23 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.282 Fit side-chains REVERT: B 284 ASN cc_start: 0.8226 (t0) cc_final: 0.7637 (t0) REVERT: A 284 ASN cc_start: 0.8002 (t0) cc_final: 0.7498 (t0) REVERT: C 284 ASN cc_start: 0.8051 (t0) cc_final: 0.7531 (t0) outliers start: 16 outliers final: 9 residues processed: 46 average time/residue: 0.3872 time to fit residues: 19.7298 Evaluate side-chains 39 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.092540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064539 restraints weight = 13616.024| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.13 r_work: 0.2632 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9003 Z= 0.131 Angle : 0.478 6.555 12219 Z= 0.274 Chirality : 0.042 0.136 1317 Planarity : 0.003 0.040 1611 Dihedral : 3.876 18.975 1239 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.44 % Allowed : 11.30 % Favored : 87.26 % 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: 0.82 (0.25), residues: 1131 helix: -3.80 (1.06), residues: 18 sheet: 1.40 (0.19), residues: 681 loop : -0.68 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.012 0.001 TYR C 113 PHE 0.017 0.001 PHE B 395 TRP 0.007 0.001 TRP C 286 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9003) covalent geometry : angle 0.47839 / 0.27 (12219) hydrogen bonds : bond 0.03200 / 2.08 ( 558) hydrogen bonds : angle 4.57574 / 3.11 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.363 Fit side-chains REVERT: B 284 ASN cc_start: 0.8260 (t0) cc_final: 0.7632 (t0) REVERT: A 141 ILE cc_start: 0.8693 (mp) cc_final: 0.8458 (pt) REVERT: A 284 ASN cc_start: 0.8033 (t0) cc_final: 0.7512 (t0) REVERT: C 284 ASN cc_start: 0.8118 (t0) cc_final: 0.7573 (t0) outliers start: 13 outliers final: 9 residues processed: 38 average time/residue: 0.3919 time to fit residues: 16.6298 Evaluate side-chains 37 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.093056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.065142 restraints weight = 13602.702| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.13 r_work: 0.2644 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9003 Z= 0.113 Angle : 0.462 5.824 12219 Z= 0.266 Chirality : 0.041 0.137 1317 Planarity : 0.002 0.040 1611 Dihedral : 3.783 18.215 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.44 % Allowed : 11.52 % Favored : 87.04 % 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: 0.85 (0.25), residues: 1131 helix: -3.75 (1.07), residues: 18 sheet: 1.39 (0.19), residues: 681 loop : -0.62 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.011 0.001 TYR C 113 PHE 0.017 0.001 PHE B 395 TRP 0.006 0.001 TRP C 286 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9003) covalent geometry : angle 0.46235 / 0.27 (12219) hydrogen bonds : bond 0.03018 / 1.97 ( 558) hydrogen bonds : angle 4.48825 / 3.06 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.238 Fit side-chains REVERT: B 284 ASN cc_start: 0.8314 (t0) cc_final: 0.7691 (t0) REVERT: A 141 ILE cc_start: 0.8637 (mp) cc_final: 0.8369 (pt) REVERT: A 284 ASN cc_start: 0.8051 (t0) cc_final: 0.7508 (t0) REVERT: C 284 ASN cc_start: 0.8176 (t0) cc_final: 0.7602 (t0) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.3449 time to fit residues: 15.5308 Evaluate side-chains 40 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066708 restraints weight = 13650.547| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.15 r_work: 0.2674 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9003 Z= 0.085 Angle : 0.442 5.479 12219 Z= 0.255 Chirality : 0.041 0.139 1317 Planarity : 0.002 0.040 1611 Dihedral : 3.617 17.221 1239 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 11.74 % Favored : 87.04 % 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: 0.88 (0.25), residues: 1131 helix: -3.64 (1.12), residues: 18 sheet: 1.38 (0.19), residues: 681 loop : -0.55 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 67 TYR 0.008 0.001 TYR C 113 PHE 0.015 0.001 PHE A 395 TRP 0.006 0.001 TRP A 286 HIS 0.002 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 9003) covalent geometry : angle 0.44167 / 0.26 (12219) hydrogen bonds : bond 0.02700 / 1.77 ( 558) hydrogen bonds : angle 4.37344 / 2.98 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.332 Fit side-chains REVERT: B 284 ASN cc_start: 0.8288 (t0) cc_final: 0.7656 (t0) REVERT: A 284 ASN cc_start: 0.7977 (t0) cc_final: 0.7418 (t0) REVERT: C 23 THR cc_start: 0.8643 (m) cc_final: 0.8329 (t) REVERT: C 170 MET cc_start: 0.6743 (mmt) cc_final: 0.6458 (mmt) REVERT: C 236 ASP cc_start: 0.8653 (t0) cc_final: 0.8330 (t0) REVERT: C 284 ASN cc_start: 0.8142 (t0) cc_final: 0.7550 (t0) outliers start: 11 outliers final: 10 residues processed: 43 average time/residue: 0.3039 time to fit residues: 14.7959 Evaluate side-chains 39 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.090578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062756 restraints weight = 13671.129| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.10 r_work: 0.2597 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9003 Z= 0.222 Angle : 0.542 8.481 12219 Z= 0.304 Chirality : 0.043 0.137 1317 Planarity : 0.003 0.038 1611 Dihedral : 4.110 18.886 1239 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.11 % Allowed : 12.62 % Favored : 86.27 % 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: 0.82 (0.25), residues: 1131 helix: -3.85 (1.04), residues: 18 sheet: 1.41 (0.19), residues: 681 loop : -0.71 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 417 TYR 0.016 0.001 TYR C 113 PHE 0.022 0.002 PHE B 395 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 9003) covalent geometry : angle 0.54230 / 0.30 (12219) hydrogen bonds : bond 0.03652 / 2.37 ( 558) hydrogen bonds : angle 4.64635 / 3.16 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.328 Fit side-chains REVERT: B 284 ASN cc_start: 0.8435 (t0) cc_final: 0.7821 (t0) REVERT: A 284 ASN cc_start: 0.8201 (t0) cc_final: 0.7671 (t0) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 0.3545 time to fit residues: 13.9962 Evaluate side-chains 34 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 108 optimal weight: 0.0980 chunk 79 optimal weight: 0.0070 chunk 15 optimal weight: 0.8980 overall best weight: 0.2254 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.095500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.067663 restraints weight = 13491.127| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.13 r_work: 0.2692 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9003 Z= 0.078 Angle : 0.463 8.618 12219 Z= 0.262 Chirality : 0.041 0.144 1317 Planarity : 0.002 0.041 1611 Dihedral : 3.611 16.550 1239 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.78 % Allowed : 12.96 % Favored : 86.27 % 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: 0.92 (0.25), residues: 1131 helix: -3.65 (1.11), residues: 18 sheet: 1.40 (0.19), residues: 681 loop : -0.50 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 67 TYR 0.007 0.001 TYR C 113 PHE 0.015 0.001 PHE A 395 TRP 0.007 0.001 TRP C 222 HIS 0.002 0.000 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.08 ( 9003) covalent geometry : angle 0.46255 / 0.26 (12219) hydrogen bonds : bond 0.02557 / 1.69 ( 558) hydrogen bonds : angle 4.34968 / 2.96 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.236 Fit side-chains REVERT: B 284 ASN cc_start: 0.8323 (t0) cc_final: 0.7697 (t0) REVERT: A 284 ASN cc_start: 0.7982 (t0) cc_final: 0.7424 (t0) REVERT: C 23 THR cc_start: 0.8691 (m) cc_final: 0.8408 (t) REVERT: C 170 MET cc_start: 0.6690 (mmt) cc_final: 0.6433 (mmt) REVERT: C 236 ASP cc_start: 0.8655 (t0) cc_final: 0.8339 (t0) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.3316 time to fit residues: 13.4601 Evaluate side-chains 34 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.090281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.062299 restraints weight = 13686.942| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.12 r_work: 0.2592 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9003 Z= 0.260 Angle : 0.566 8.174 12219 Z= 0.315 Chirality : 0.043 0.136 1317 Planarity : 0.003 0.038 1611 Dihedral : 4.149 19.034 1239 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.55 % Allowed : 13.29 % Favored : 86.16 % 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: 0.78 (0.25), residues: 1131 helix: -3.82 (1.06), residues: 18 sheet: 1.42 (0.19), residues: 675 loop : -0.77 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 417 TYR 0.016 0.001 TYR C 113 PHE 0.023 0.002 PHE B 395 TRP 0.008 0.001 TRP A 249 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 ( 9003) covalent geometry : angle 0.56568 / 0.32 (12219) hydrogen bonds : bond 0.03712 / 2.41 ( 558) hydrogen bonds : angle 4.63283 / 3.15 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.324 Fit side-chains REVERT: B 284 ASN cc_start: 0.8475 (t0) cc_final: 0.7901 (t0) REVERT: A 284 ASN cc_start: 0.8178 (t0) cc_final: 0.7636 (t0) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.3992 time to fit residues: 14.4044 Evaluate side-chains 29 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain C residue 157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 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 = 0.3248 r_free = 0.3248 target = 0.092754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.064779 restraints weight = 13398.885| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.12 r_work: 0.2640 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9003 Z= 0.123 Angle : 0.502 8.163 12219 Z= 0.282 Chirality : 0.041 0.137 1317 Planarity : 0.002 0.040 1611 Dihedral : 3.871 17.966 1239 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.78 % Allowed : 13.18 % Favored : 86.05 % 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: 0.84 (0.25), residues: 1131 helix: -3.76 (1.08), residues: 18 sheet: 1.41 (0.19), residues: 675 loop : -0.65 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.010 0.001 TYR A 113 PHE 0.017 0.001 PHE B 395 TRP 0.006 0.001 TRP C 286 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9003) covalent geometry : angle 0.50217 / 0.28 (12219) hydrogen bonds : bond 0.03014 / 1.97 ( 558) hydrogen bonds : angle 4.47752 / 3.04 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.83 seconds wall clock time: 33 minutes 50.01 seconds (2030.01 seconds total)