Starting phenix.real_space_refine on Tue Jan 13 14:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byt_16333/01_2026/8byt_16333.map" } resolution = 2.78 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= 0.014 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 9 5.16 5 C 4383 2.51 5 N 1257 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7077 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2359 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 2, 'TRANS': 305} Restraints were copied for chains: B, C Time building chain proxies: 1.56, per 1000 atoms: 0.22 Number of scatterers: 7077 At special positions: 0 Unit cell: (93.562, 92.988, 59.122, 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 9 16.00 O 1428 8.00 N 1257 7.00 C 4383 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: 0.63 Conformation dependent library (CDL) restraints added in 254.1 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 6 sheets defined 1.6% alpha, 59.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.815A pdb=" N ALA A 243 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.815A pdb=" N ALA B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.816A pdb=" N ALA C 243 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 130 removed outlier: 3.540A pdb=" N ARG A 185 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 167 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE A 183 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 23.932A pdb=" N THR A 182 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 18.708A pdb=" N THR A 206 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 12.792A pdb=" N ASP A 184 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 204 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR A 213 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 376 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 400 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 130 removed outlier: 3.540A pdb=" N ARG B 185 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS B 167 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE B 183 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 23.932A pdb=" N THR B 182 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 18.709A pdb=" N THR B 206 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 12.792A pdb=" N ASP B 184 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN B 204 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR B 213 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 376 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B 400 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 130 removed outlier: 3.540A pdb=" N ARG C 185 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS C 167 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 183 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 23.933A pdb=" N THR C 182 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 18.709A pdb=" N THR C 206 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 12.792A pdb=" N ASP C 184 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN C 204 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 213 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 400 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 279 through 283 438 hydrogen bonds defined for protein. 1233 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: 0.90 Time building geometry restraints manager: 0.82 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: 2412 1.34 - 1.46: 1544 1.46 - 1.57: 3238 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 7212 Sorted by residual: bond pdb=" N GLY B 391 " pdb=" CA GLY B 391 " ideal model delta sigma weight residual 1.454 1.448 0.007 9.90e-03 1.02e+04 4.51e-01 bond pdb=" N GLY C 391 " pdb=" CA GLY C 391 " ideal model delta sigma weight residual 1.454 1.448 0.006 9.90e-03 1.02e+04 3.99e-01 bond pdb=" N GLY A 391 " pdb=" CA GLY A 391 " ideal model delta sigma weight residual 1.454 1.448 0.006 9.90e-03 1.02e+04 3.87e-01 bond pdb=" N GLY C 261 " pdb=" CA GLY C 261 " ideal model delta sigma weight residual 1.449 1.456 -0.007 1.14e-02 7.69e+03 3.67e-01 bond pdb=" N GLY A 261 " pdb=" CA GLY A 261 " ideal model delta sigma weight residual 1.449 1.456 -0.007 1.14e-02 7.69e+03 3.41e-01 ... (remaining 7207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 9449 1.05 - 2.09: 247 2.09 - 3.14: 19 3.14 - 4.18: 6 4.18 - 5.23: 2 Bond angle restraints: 9723 Sorted by residual: angle pdb=" N GLY A 236 " pdb=" CA GLY A 236 " pdb=" C GLY A 236 " ideal model delta sigma weight residual 110.58 114.71 -4.13 1.35e+00 5.49e-01 9.36e+00 angle pdb=" N GLY B 236 " pdb=" CA GLY B 236 " pdb=" C GLY B 236 " ideal model delta sigma weight residual 110.58 114.70 -4.12 1.35e+00 5.49e-01 9.30e+00 angle pdb=" N GLY C 236 " pdb=" CA GLY C 236 " pdb=" C GLY C 236 " ideal model delta sigma weight residual 110.58 114.69 -4.11 1.35e+00 5.49e-01 9.27e+00 angle pdb=" C ASN B 226 " pdb=" N ASP B 227 " pdb=" CA ASP B 227 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 angle pdb=" C ASN A 226 " pdb=" N ASP A 227 " pdb=" CA ASP A 227 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.45e+00 ... (remaining 9718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3987 17.97 - 35.94: 134 35.94 - 53.91: 34 53.91 - 71.88: 6 71.88 - 89.85: 6 Dihedral angle restraints: 4167 sinusoidal: 1578 harmonic: 2589 Sorted by residual: dihedral pdb=" CA ASP C 383 " pdb=" CB ASP C 383 " pdb=" CG ASP C 383 " pdb=" OD1 ASP C 383 " ideal model delta sinusoidal sigma weight residual -30.00 -82.42 52.42 1 2.00e+01 2.50e-03 9.36e+00 dihedral pdb=" CA ASP B 383 " pdb=" CB ASP B 383 " pdb=" CG ASP B 383 " pdb=" OD1 ASP B 383 " ideal model delta sinusoidal sigma weight residual -30.00 -82.40 52.40 1 2.00e+01 2.50e-03 9.36e+00 dihedral pdb=" CA ASP A 383 " pdb=" CB ASP A 383 " pdb=" CG ASP A 383 " pdb=" OD1 ASP A 383 " ideal model delta sinusoidal sigma weight residual -30.00 -82.38 52.38 1 2.00e+01 2.50e-03 9.35e+00 ... (remaining 4164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 579 0.027 - 0.053: 250 0.053 - 0.080: 67 0.080 - 0.107: 59 0.107 - 0.133: 26 Chirality restraints: 981 Sorted by residual: chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE B 357 " pdb=" N ILE B 357 " pdb=" C ILE B 357 " pdb=" CB ILE B 357 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE C 357 " pdb=" N ILE C 357 " pdb=" C ILE C 357 " pdb=" CB ILE C 357 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 978 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 355 " 0.012 5.00e-02 4.00e+02 1.80e-02 5.21e-01 pdb=" N PRO C 356 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 356 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 356 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 355 " 0.012 5.00e-02 4.00e+02 1.80e-02 5.20e-01 pdb=" N PRO B 356 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 355 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO A 356 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.010 5.00e-02 4.00e+02 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1337 2.78 - 3.31: 5899 3.31 - 3.84: 11711 3.84 - 4.37: 14364 4.37 - 4.90: 26604 Nonbonded interactions: 59915 Sorted by model distance: nonbonded pdb=" OH TYR B 213 " pdb=" O THR B 216 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR C 213 " pdb=" O THR C 216 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O THR A 216 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 366 " pdb=" OG SER A 409 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR B 366 " pdb=" OG SER B 409 " model vdw 2.310 3.040 ... (remaining 59910 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 'A' selection = chain 'B' 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: 15.180 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.860 Find NCS groups from input model: 0.060 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.002 0.014 7212 Z= 0.088 Angle : 0.416 5.231 9723 Z= 0.249 Chirality : 0.041 0.133 981 Planarity : 0.002 0.018 1305 Dihedral : 10.691 89.854 2559 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.38 (0.30), residues: 918 helix: None (None), residues: 0 sheet: 0.82 (0.23), residues: 576 loop : -0.69 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 126 TYR 0.006 0.001 TYR A 348 PHE 0.010 0.001 PHE A 217 TRP 0.006 0.001 TRP C 342 HIS 0.001 0.000 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 7212) covalent geometry : angle 0.41592 ( 9723) hydrogen bonds : bond 0.16048 ( 438) hydrogen bonds : angle 8.20029 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.205 Fit side-chains REVERT: A 159 LYS cc_start: 0.6623 (mttt) cc_final: 0.6123 (pttt) REVERT: A 262 LYS cc_start: 0.7365 (mmtm) cc_final: 0.7162 (mmtm) REVERT: A 338 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7707 (mtmt) REVERT: A 399 ASN cc_start: 0.8189 (t0) cc_final: 0.7729 (m-40) REVERT: A 413 ARG cc_start: 0.7771 (mtp85) cc_final: 0.6643 (mtm110) REVERT: B 159 LYS cc_start: 0.6533 (mttt) cc_final: 0.5998 (pttt) REVERT: B 262 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7199 (mmtm) REVERT: B 338 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7718 (mtmt) REVERT: B 413 ARG cc_start: 0.7764 (mtp85) cc_final: 0.6579 (mtm110) REVERT: C 159 LYS cc_start: 0.6538 (mttt) cc_final: 0.5992 (pttt) REVERT: C 338 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7645 (mtmt) REVERT: C 413 ARG cc_start: 0.7770 (mtp85) cc_final: 0.6653 (mtm110) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.6222 time to fit residues: 79.5741 Evaluate side-chains 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 246 ASN A 283 HIS A 417 ASN B 153 ASN B 246 ASN B 283 HIS B 417 ASN C 153 ASN C 161 GLN C 180 GLN C 246 ASN C 283 HIS C 417 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101100 restraints weight = 7973.675| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.61 r_work: 0.3025 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7212 Z= 0.189 Angle : 0.544 5.286 9723 Z= 0.311 Chirality : 0.044 0.132 981 Planarity : 0.003 0.021 1305 Dihedral : 4.294 11.488 1014 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.34 % Allowed : 8.40 % Favored : 89.26 % 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: -0.05 (0.29), residues: 918 helix: None (None), residues: 0 sheet: 0.27 (0.22), residues: 600 loop : -0.44 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 413 TYR 0.010 0.002 TYR B 187 PHE 0.017 0.002 PHE C 217 TRP 0.013 0.002 TRP B 325 HIS 0.004 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7212) covalent geometry : angle 0.54450 ( 9723) hydrogen bonds : bond 0.03478 ( 438) hydrogen bonds : angle 5.96488 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.273 Fit side-chains REVERT: A 159 LYS cc_start: 0.7130 (mttt) cc_final: 0.6742 (pttt) REVERT: A 343 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7508 (t70) REVERT: B 159 LYS cc_start: 0.7124 (mttt) cc_final: 0.6659 (pttt) REVERT: B 262 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7701 (mmtm) REVERT: C 159 LYS cc_start: 0.7153 (mttt) cc_final: 0.6665 (pttt) REVERT: C 161 GLN cc_start: 0.8365 (pt0) cc_final: 0.8015 (pt0) REVERT: C 180 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7579 (mm-40) REVERT: C 230 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7921 (mt0) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.6458 time to fit residues: 68.3270 Evaluate side-chains 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099292 restraints weight = 7894.369| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.3007 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7212 Z= 0.195 Angle : 0.534 5.200 9723 Z= 0.304 Chirality : 0.044 0.136 981 Planarity : 0.003 0.025 1305 Dihedral : 4.487 11.966 1014 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.89 % Allowed : 9.50 % Favored : 87.60 % 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: -0.12 (0.29), residues: 918 helix: None (None), residues: 0 sheet: 0.19 (0.22), residues: 600 loop : -0.40 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.008 0.002 TYR A 187 PHE 0.015 0.002 PHE C 217 TRP 0.015 0.002 TRP B 325 HIS 0.003 0.002 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7212) covalent geometry : angle 0.53371 ( 9723) hydrogen bonds : bond 0.03298 ( 438) hydrogen bonds : angle 5.73785 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.253 Fit side-chains REVERT: A 159 LYS cc_start: 0.7111 (mttt) cc_final: 0.6684 (pttt) REVERT: A 343 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7568 (t70) REVERT: B 159 LYS cc_start: 0.7181 (mttt) cc_final: 0.6667 (pttt) REVERT: B 262 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7666 (mmtm) REVERT: B 343 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7280 (t70) REVERT: C 159 LYS cc_start: 0.7159 (mttt) cc_final: 0.6619 (pttt) REVERT: C 161 GLN cc_start: 0.8354 (pt0) cc_final: 0.7973 (pt0) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 0.5970 time to fit residues: 63.4447 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 221 GLN B 223 ASN B 351 GLN C 128 GLN C 180 GLN C 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097231 restraints weight = 8091.984| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.62 r_work: 0.2969 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7212 Z= 0.263 Angle : 0.584 6.520 9723 Z= 0.329 Chirality : 0.046 0.135 981 Planarity : 0.003 0.025 1305 Dihedral : 4.794 12.767 1014 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.99 % Allowed : 9.78 % Favored : 86.23 % 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: -0.26 (0.28), residues: 918 helix: None (None), residues: 0 sheet: 0.11 (0.21), residues: 597 loop : -0.50 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.011 0.002 TYR B 235 PHE 0.016 0.002 PHE C 217 TRP 0.019 0.002 TRP B 325 HIS 0.004 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 7212) covalent geometry : angle 0.58400 ( 9723) hydrogen bonds : bond 0.03344 ( 438) hydrogen bonds : angle 5.83858 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.285 Fit side-chains REVERT: A 159 LYS cc_start: 0.7139 (mttt) cc_final: 0.6674 (pttt) REVERT: A 180 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7514 (mm-40) REVERT: A 230 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: A 343 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7619 (t70) REVERT: B 159 LYS cc_start: 0.7230 (mttt) cc_final: 0.6693 (pttt) REVERT: B 262 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7679 (mmtm) REVERT: C 159 LYS cc_start: 0.7155 (mttt) cc_final: 0.6603 (pttt) REVERT: C 161 GLN cc_start: 0.8370 (pt0) cc_final: 0.7964 (pt0) REVERT: C 343 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7477 (t70) outliers start: 29 outliers final: 12 residues processed: 101 average time/residue: 0.6248 time to fit residues: 66.3356 Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 221 GLN A 223 ASN A 351 GLN B 351 GLN C 221 GLN C 223 ASN C 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098942 restraints weight = 8103.047| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.62 r_work: 0.3020 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7212 Z= 0.139 Angle : 0.491 4.579 9723 Z= 0.282 Chirality : 0.043 0.136 981 Planarity : 0.002 0.016 1305 Dihedral : 4.457 12.532 1014 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.17 % Allowed : 11.57 % Favored : 85.26 % 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: -0.29 (0.28), residues: 918 helix: None (None), residues: 0 sheet: 0.04 (0.21), residues: 603 loop : -0.41 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 413 TYR 0.009 0.001 TYR C 256 PHE 0.012 0.001 PHE A 217 TRP 0.015 0.001 TRP B 325 HIS 0.003 0.002 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7212) covalent geometry : angle 0.49106 ( 9723) hydrogen bonds : bond 0.02947 ( 438) hydrogen bonds : angle 5.47894 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.262 Fit side-chains REVERT: A 159 LYS cc_start: 0.7100 (mttt) cc_final: 0.6656 (pttt) REVERT: A 412 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8230 (p90) REVERT: B 159 LYS cc_start: 0.7190 (mttt) cc_final: 0.6650 (pttt) REVERT: B 343 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7362 (t70) REVERT: C 159 LYS cc_start: 0.7148 (mttt) cc_final: 0.6612 (pttt) REVERT: C 161 GLN cc_start: 0.8364 (pt0) cc_final: 0.7924 (pt0) outliers start: 23 outliers final: 10 residues processed: 103 average time/residue: 0.6272 time to fit residues: 67.7824 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 412 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098145 restraints weight = 8091.027| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.63 r_work: 0.3000 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7212 Z= 0.200 Angle : 0.540 5.332 9723 Z= 0.304 Chirality : 0.044 0.134 981 Planarity : 0.003 0.017 1305 Dihedral : 4.625 12.616 1014 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.44 % Allowed : 13.36 % Favored : 83.20 % 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: -0.35 (0.28), residues: 918 helix: None (None), residues: 0 sheet: 0.01 (0.21), residues: 600 loop : -0.48 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.009 0.002 TYR C 256 PHE 0.013 0.002 PHE B 217 TRP 0.016 0.002 TRP B 325 HIS 0.003 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7212) covalent geometry : angle 0.53969 ( 9723) hydrogen bonds : bond 0.03051 ( 438) hydrogen bonds : angle 5.55769 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.289 Fit side-chains REVERT: A 159 LYS cc_start: 0.7153 (mttt) cc_final: 0.6680 (pttt) REVERT: A 161 GLN cc_start: 0.8225 (pt0) cc_final: 0.7810 (mp10) REVERT: A 412 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8205 (p90) REVERT: B 159 LYS cc_start: 0.7216 (mttt) cc_final: 0.6673 (pttt) REVERT: B 161 GLN cc_start: 0.8288 (pt0) cc_final: 0.7898 (mp10) REVERT: B 343 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7042 (t0) REVERT: C 159 LYS cc_start: 0.7132 (mttt) cc_final: 0.6592 (pttt) REVERT: C 161 GLN cc_start: 0.8362 (pt0) cc_final: 0.7953 (pt0) outliers start: 25 outliers final: 10 residues processed: 101 average time/residue: 0.6989 time to fit residues: 73.7186 Evaluate side-chains 98 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 0.0060 chunk 60 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099616 restraints weight = 7972.024| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.62 r_work: 0.3019 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7212 Z= 0.118 Angle : 0.480 5.183 9723 Z= 0.274 Chirality : 0.043 0.136 981 Planarity : 0.002 0.009 1305 Dihedral : 4.344 12.382 1014 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.34 % Allowed : 15.01 % Favored : 82.64 % 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: -0.33 (0.28), residues: 918 helix: None (None), residues: 0 sheet: -0.01 (0.21), residues: 603 loop : -0.40 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 413 TYR 0.010 0.001 TYR C 256 PHE 0.011 0.001 PHE A 217 TRP 0.015 0.001 TRP B 325 HIS 0.002 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7212) covalent geometry : angle 0.48031 ( 9723) hydrogen bonds : bond 0.02784 ( 438) hydrogen bonds : angle 5.29248 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.271 Fit side-chains REVERT: A 159 LYS cc_start: 0.7120 (mttt) cc_final: 0.6650 (pttt) REVERT: A 161 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: A 412 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8244 (p90) REVERT: A 419 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8499 (tttm) REVERT: B 159 LYS cc_start: 0.7176 (mttt) cc_final: 0.6621 (pttt) REVERT: B 161 GLN cc_start: 0.8267 (pt0) cc_final: 0.7889 (mp10) REVERT: C 159 LYS cc_start: 0.7074 (mttt) cc_final: 0.6573 (pttt) REVERT: C 161 GLN cc_start: 0.8355 (pt0) cc_final: 0.7942 (pt0) outliers start: 17 outliers final: 8 residues processed: 107 average time/residue: 0.6003 time to fit residues: 67.5591 Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 412 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 223 ASN B 351 GLN C 180 GLN C 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098955 restraints weight = 8080.661| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.63 r_work: 0.3017 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7212 Z= 0.150 Angle : 0.497 4.905 9723 Z= 0.282 Chirality : 0.043 0.133 981 Planarity : 0.002 0.012 1305 Dihedral : 4.401 12.490 1014 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.20 % Allowed : 15.98 % Favored : 81.82 % 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: -0.33 (0.28), residues: 918 helix: None (None), residues: 0 sheet: 0.00 (0.21), residues: 603 loop : -0.42 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 413 TYR 0.009 0.001 TYR C 256 PHE 0.012 0.001 PHE A 217 TRP 0.014 0.001 TRP B 325 HIS 0.003 0.002 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7212) covalent geometry : angle 0.49713 ( 9723) hydrogen bonds : bond 0.02835 ( 438) hydrogen bonds : angle 5.30474 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.279 Fit side-chains REVERT: A 159 LYS cc_start: 0.7135 (mttt) cc_final: 0.6663 (pttt) REVERT: A 161 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: A 230 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 412 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8210 (p90) REVERT: A 419 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (tttm) REVERT: B 159 LYS cc_start: 0.7194 (mttt) cc_final: 0.6624 (pttt) REVERT: B 161 GLN cc_start: 0.8281 (pt0) cc_final: 0.7904 (mp10) REVERT: C 159 LYS cc_start: 0.7067 (mttt) cc_final: 0.6560 (pttt) REVERT: C 161 GLN cc_start: 0.8352 (pt0) cc_final: 0.7934 (pt0) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.6294 time to fit residues: 67.3666 Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 412 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096629 restraints weight = 8081.402| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.61 r_work: 0.2988 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7212 Z= 0.241 Angle : 0.567 5.956 9723 Z= 0.317 Chirality : 0.045 0.133 981 Planarity : 0.003 0.019 1305 Dihedral : 4.706 12.878 1014 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.03 % Allowed : 15.70 % Favored : 81.27 % 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: -0.39 (0.28), residues: 918 helix: None (None), residues: 0 sheet: -0.02 (0.21), residues: 600 loop : -0.48 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.010 0.002 TYR B 235 PHE 0.015 0.002 PHE C 217 TRP 0.016 0.002 TRP B 325 HIS 0.003 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 7212) covalent geometry : angle 0.56730 ( 9723) hydrogen bonds : bond 0.03144 ( 438) hydrogen bonds : angle 5.55516 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.274 Fit side-chains REVERT: A 159 LYS cc_start: 0.7155 (mttt) cc_final: 0.6683 (pttt) REVERT: A 161 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: A 230 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: A 412 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8209 (p90) REVERT: B 159 LYS cc_start: 0.7198 (mttt) cc_final: 0.6652 (pttt) REVERT: B 161 GLN cc_start: 0.8299 (pt0) cc_final: 0.7949 (mp10) REVERT: B 180 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7622 (mm-40) REVERT: C 159 LYS cc_start: 0.7113 (mttt) cc_final: 0.6591 (pttt) REVERT: C 343 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7493 (t70) outliers start: 22 outliers final: 9 residues processed: 99 average time/residue: 0.6699 time to fit residues: 69.4376 Evaluate side-chains 104 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098111 restraints weight = 8054.458| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.61 r_work: 0.2998 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7212 Z= 0.194 Angle : 0.537 5.247 9723 Z= 0.302 Chirality : 0.044 0.136 981 Planarity : 0.002 0.015 1305 Dihedral : 4.644 12.853 1014 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.20 % Allowed : 16.80 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 918 helix: None (None), residues: 0 sheet: -0.05 (0.21), residues: 600 loop : -0.46 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 413 TYR 0.009 0.002 TYR C 235 PHE 0.013 0.002 PHE A 217 TRP 0.016 0.002 TRP B 325 HIS 0.003 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7212) covalent geometry : angle 0.53705 ( 9723) hydrogen bonds : bond 0.03036 ( 438) hydrogen bonds : angle 5.49991 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.247 Fit side-chains REVERT: A 159 LYS cc_start: 0.7136 (mttt) cc_final: 0.6642 (pttt) REVERT: A 161 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: A 230 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: A 412 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8207 (p90) REVERT: B 159 LYS cc_start: 0.7166 (mttt) cc_final: 0.6629 (pttt) REVERT: B 161 GLN cc_start: 0.8279 (pt0) cc_final: 0.7938 (mp10) REVERT: C 159 LYS cc_start: 0.7101 (mttt) cc_final: 0.6596 (pttt) REVERT: C 161 GLN cc_start: 0.8346 (pt0) cc_final: 0.7995 (mp10) REVERT: C 343 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7492 (t70) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.6368 time to fit residues: 63.3454 Evaluate side-chains 101 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099698 restraints weight = 8007.970| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.62 r_work: 0.3032 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7212 Z= 0.113 Angle : 0.476 4.861 9723 Z= 0.273 Chirality : 0.043 0.139 981 Planarity : 0.002 0.010 1305 Dihedral : 4.380 12.634 1014 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.79 % Allowed : 17.08 % Favored : 81.13 % 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: -0.40 (0.28), residues: 918 helix: None (None), residues: 0 sheet: -0.08 (0.21), residues: 603 loop : -0.39 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 413 TYR 0.010 0.001 TYR B 256 PHE 0.010 0.001 PHE C 217 TRP 0.017 0.001 TRP A 325 HIS 0.002 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7212) covalent geometry : angle 0.47649 ( 9723) hydrogen bonds : bond 0.02753 ( 438) hydrogen bonds : angle 5.27073 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.97 seconds wall clock time: 45 minutes 57.82 seconds (2757.82 seconds total)