Starting phenix.real_space_refine on Wed Feb 4 02:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e08_47352/02_2026/9e08_47352.map" } resolution = 2.1 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= 0.012 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 46 5.16 5 C 5294 2.51 5 N 1432 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8304 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4152 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 31, 'TRANS': 481} Restraints were copied for chains: B Time building chain proxies: 2.74, per 1000 atoms: 0.33 Number of scatterers: 8304 At special positions: 0 Unit cell: (135.135, 83.853, 69.993, 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 46 16.00 O 1532 8.00 N 1432 7.00 C 5294 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 306.6 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 10.9% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 538 through 542 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.579A pdb=" N MET A 118 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 117 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE A 219 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 119 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 214 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP A 236 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 216 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR A 230 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 196 removed outlier: 7.863A pdb=" N GLY A 273 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA A 275 " --> pdb=" O TRP A 394 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TRP A 394 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 283 removed outlier: 6.241A pdb=" N ILE A 298 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 340 removed outlier: 5.895A pdb=" N GLN A 533 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 434 removed outlier: 6.534A pdb=" N ASP A 458 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 430 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA A 456 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 432 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 454 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 426 through 434 removed outlier: 6.534A pdb=" N ASP A 458 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 430 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA A 456 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 432 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 454 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 43 through 44 removed outlier: 4.579A pdb=" N MET B 118 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG B 117 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE B 219 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 119 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 214 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 236 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 216 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 230 " --> pdb=" O ASP B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'B' and resid 102 through 105 Processing sheet with id=AB4, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB5, first strand: chain 'B' and resid 195 through 196 removed outlier: 7.862A pdb=" N GLY B 273 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA B 275 " --> pdb=" O TRP B 394 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TRP B 394 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.241A pdb=" N ILE B 298 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.895A pdb=" N GLN B 533 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 426 through 434 removed outlier: 6.534A pdb=" N ASP B 458 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 430 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 456 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 432 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 454 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 426 through 434 removed outlier: 6.534A pdb=" N ASP B 458 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 430 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 456 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 432 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 454 " --> pdb=" O THR B 432 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 774 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: 1.35 Time building geometry restraints manager: 0.85 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: 2730 1.34 - 1.46: 2084 1.46 - 1.58: 3660 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8552 Sorted by residual: bond pdb=" CA THR A 147 " pdb=" CB THR A 147 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.61e-01 bond pdb=" CA THR B 147 " pdb=" CB THR B 147 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.69e-02 3.50e+03 7.27e-01 bond pdb=" N THR A 510 " pdb=" CA THR A 510 " ideal model delta sigma weight residual 1.462 1.471 -0.010 1.48e-02 4.57e+03 4.16e-01 bond pdb=" N THR B 510 " pdb=" CA THR B 510 " ideal model delta sigma weight residual 1.462 1.471 -0.009 1.48e-02 4.57e+03 3.91e-01 bond pdb=" CB ASP A 155 " pdb=" CG ASP A 155 " ideal model delta sigma weight residual 1.516 1.531 -0.015 2.50e-02 1.60e+03 3.78e-01 ... (remaining 8547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 11366 1.08 - 2.17: 170 2.17 - 3.25: 64 3.25 - 4.33: 0 4.33 - 5.41: 8 Bond angle restraints: 11608 Sorted by residual: angle pdb=" C ASP A 146 " pdb=" N THR A 147 " pdb=" CA THR A 147 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" C ASP B 146 " pdb=" N THR B 147 " pdb=" CA THR B 147 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ALA B 180 " ideal model delta sigma weight residual 114.85 116.60 -1.75 9.50e-01 1.11e+00 3.39e+00 angle pdb=" CA THR B 147 " pdb=" CB THR B 147 " pdb=" CG2 THR B 147 " ideal model delta sigma weight residual 110.50 113.62 -3.12 1.70e+00 3.46e-01 3.36e+00 angle pdb=" CA THR A 147 " pdb=" CB THR A 147 " pdb=" CG2 THR A 147 " ideal model delta sigma weight residual 110.50 113.61 -3.11 1.70e+00 3.46e-01 3.35e+00 ... (remaining 11603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 4247 16.70 - 33.40: 553 33.40 - 50.10: 170 50.10 - 66.81: 44 66.81 - 83.51: 20 Dihedral angle restraints: 5034 sinusoidal: 2056 harmonic: 2978 Sorted by residual: dihedral pdb=" CA ASP A 302 " pdb=" CB ASP A 302 " pdb=" CG ASP A 302 " pdb=" OD1 ASP A 302 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP B 302 " pdb=" CB ASP B 302 " pdb=" CG ASP B 302 " pdb=" OD1 ASP B 302 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" N LEU B 531 " pdb=" CA LEU B 531 " pdb=" CB LEU B 531 " pdb=" CG LEU B 531 " ideal model delta sinusoidal sigma weight residual -60.00 -118.40 58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 601 0.024 - 0.047: 357 0.047 - 0.070: 109 0.070 - 0.094: 42 0.094 - 0.117: 69 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA THR A 510 " pdb=" N THR A 510 " pdb=" C THR A 510 " pdb=" CB THR A 510 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE B 499 " pdb=" N ILE B 499 " pdb=" C ILE B 499 " pdb=" CB ILE B 499 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE B 298 " pdb=" N ILE B 298 " pdb=" C ILE B 298 " pdb=" CB ILE B 298 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1175 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 147 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C THR A 147 " -0.035 2.00e-02 2.50e+03 pdb=" O THR A 147 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 148 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 147 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C THR B 147 " 0.035 2.00e-02 2.50e+03 pdb=" O THR B 147 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS B 148 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 77 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 78 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.020 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2244 2.81 - 3.33: 6724 3.33 - 3.85: 14484 3.85 - 4.38: 17831 4.38 - 4.90: 29869 Nonbonded interactions: 71152 Sorted by model distance: nonbonded pdb=" OD2 ASP A 345 " pdb=" OG SER A 347 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP B 345 " pdb=" OG SER B 347 " model vdw 2.282 3.040 nonbonded pdb=" N ASP B 187 " pdb=" OD1 ASP B 187 " model vdw 2.341 3.120 nonbonded pdb=" N ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.341 3.120 nonbonded pdb=" OH TYR B 356 " pdb=" OE1 GLU B 385 " model vdw 2.345 3.040 ... (remaining 71147 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10.890 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.040 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 0.019 8552 Z= 0.086 Angle : 0.411 5.414 11608 Z= 0.217 Chirality : 0.040 0.117 1178 Planarity : 0.003 0.035 1528 Dihedral : 17.332 83.507 3126 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.49 % Allowed : 25.17 % Favored : 73.33 % 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 (0.27), residues: 1022 helix: 0.39 (0.64), residues: 68 sheet: 1.30 (0.28), residues: 382 loop : -0.55 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 431 TYR 0.006 0.001 TYR B 140 PHE 0.007 0.001 PHE A 119 TRP 0.005 0.001 TRP B 530 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 8552) covalent geometry : angle 0.41127 (11608) hydrogen bonds : bond 0.22120 ( 290) hydrogen bonds : angle 8.29420 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 411 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: B 129 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7745 (mtp85) outliers start: 13 outliers final: 7 residues processed: 233 average time/residue: 0.5873 time to fit residues: 144.0562 Evaluate side-chains 231 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 524 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 271 GLN A 327 ASN A 533 GLN B 271 GLN B 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.115185 restraints weight = 10014.668| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.20 r_work: 0.3623 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8552 Z= 0.223 Angle : 0.552 4.900 11608 Z= 0.298 Chirality : 0.046 0.157 1178 Planarity : 0.005 0.056 1528 Dihedral : 5.461 92.447 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.60 % Allowed : 22.64 % Favored : 72.76 % 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: 0.21 (0.26), residues: 1022 helix: 0.73 (0.67), residues: 68 sheet: 1.24 (0.28), residues: 378 loop : -0.72 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 44 TYR 0.013 0.002 TYR A 140 PHE 0.011 0.002 PHE A 119 TRP 0.009 0.002 TRP B 414 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8552) covalent geometry : angle 0.55186 (11608) hydrogen bonds : bond 0.04705 ( 290) hydrogen bonds : angle 6.15882 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 401 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8311 (mmtt) outliers start: 40 outliers final: 16 residues processed: 251 average time/residue: 0.5963 time to fit residues: 157.5280 Evaluate side-chains 242 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.114348 restraints weight = 9996.745| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.13 r_work: 0.3619 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8552 Z= 0.190 Angle : 0.519 4.933 11608 Z= 0.281 Chirality : 0.045 0.144 1178 Planarity : 0.005 0.048 1528 Dihedral : 4.544 34.428 1142 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.22 % Allowed : 22.30 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1022 helix: 0.86 (0.68), residues: 68 sheet: 1.11 (0.27), residues: 378 loop : -0.82 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.011 0.001 TYR B 140 PHE 0.010 0.001 PHE B 164 TRP 0.011 0.001 TRP B 414 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8552) covalent geometry : angle 0.51929 (11608) hydrogen bonds : bond 0.04319 ( 290) hydrogen bonds : angle 5.92459 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.328 Fit side-chains REVERT: B 369 LYS cc_start: 0.8353 (mmtp) cc_final: 0.8012 (mmtp) REVERT: B 401 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8276 (mmtt) outliers start: 28 outliers final: 14 residues processed: 236 average time/residue: 0.5968 time to fit residues: 148.1732 Evaluate side-chains 237 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 98 optimal weight: 0.0000 chunk 29 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114495 restraints weight = 10209.623| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.14 r_work: 0.3621 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8552 Z= 0.156 Angle : 0.504 4.901 11608 Z= 0.272 Chirality : 0.044 0.134 1178 Planarity : 0.005 0.048 1528 Dihedral : 4.465 29.514 1142 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.79 % Allowed : 21.49 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1022 helix: 0.96 (0.67), residues: 68 sheet: 1.08 (0.28), residues: 368 loop : -0.85 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 431 TYR 0.009 0.001 TYR B 518 PHE 0.010 0.001 PHE B 164 TRP 0.010 0.001 TRP B 414 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8552) covalent geometry : angle 0.50385 (11608) hydrogen bonds : bond 0.03842 ( 290) hydrogen bonds : angle 5.69862 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.329 Fit side-chains REVERT: B 369 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7997 (mmtp) REVERT: B 401 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8279 (mmtt) outliers start: 33 outliers final: 22 residues processed: 240 average time/residue: 0.6347 time to fit residues: 160.2077 Evaluate side-chains 257 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 350 GLN A 522 GLN B 348 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.121415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113258 restraints weight = 10117.245| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.17 r_work: 0.3599 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8552 Z= 0.220 Angle : 0.538 4.992 11608 Z= 0.290 Chirality : 0.046 0.161 1178 Planarity : 0.005 0.053 1528 Dihedral : 4.675 25.361 1142 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.91 % Allowed : 21.84 % Favored : 74.25 % 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: -0.09 (0.26), residues: 1022 helix: 0.84 (0.67), residues: 68 sheet: 1.13 (0.28), residues: 360 loop : -0.98 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 431 TYR 0.012 0.002 TYR A 190 PHE 0.012 0.002 PHE B 246 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 8552) covalent geometry : angle 0.53782 (11608) hydrogen bonds : bond 0.04080 ( 290) hydrogen bonds : angle 5.73883 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.333 Fit side-chains REVERT: A 270 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8182 (ptpt) REVERT: B 369 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8081 (mmtp) REVERT: B 401 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8275 (mmtt) outliers start: 34 outliers final: 20 residues processed: 249 average time/residue: 0.7149 time to fit residues: 186.9042 Evaluate side-chains 257 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 13 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 82 ASN B 348 HIS B 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.114901 restraints weight = 10128.593| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.13 r_work: 0.3626 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8552 Z= 0.123 Angle : 0.493 5.659 11608 Z= 0.266 Chirality : 0.044 0.129 1178 Planarity : 0.005 0.048 1528 Dihedral : 4.403 22.150 1142 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.76 % Allowed : 22.76 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1022 helix: 0.99 (0.67), residues: 68 sheet: 0.97 (0.27), residues: 374 loop : -0.92 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 44 TYR 0.009 0.001 TYR B 518 PHE 0.011 0.001 PHE B 164 TRP 0.011 0.001 TRP A 530 HIS 0.006 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8552) covalent geometry : angle 0.49331 (11608) hydrogen bonds : bond 0.03520 ( 290) hydrogen bonds : angle 5.54996 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.346 Fit side-chains REVERT: B 44 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7930 (ttt90) REVERT: B 369 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8008 (mmtp) outliers start: 24 outliers final: 14 residues processed: 251 average time/residue: 0.6473 time to fit residues: 170.9414 Evaluate side-chains 250 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 82 ASN B 327 ASN B 333 ASN B 348 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113878 restraints weight = 10165.662| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.14 r_work: 0.3612 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8552 Z= 0.178 Angle : 0.515 4.876 11608 Z= 0.278 Chirality : 0.045 0.146 1178 Planarity : 0.005 0.048 1528 Dihedral : 4.488 23.098 1140 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 23.45 % Favored : 73.91 % 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 (0.26), residues: 1022 helix: 0.91 (0.68), residues: 68 sheet: 1.13 (0.27), residues: 356 loop : -1.01 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 44 TYR 0.011 0.001 TYR B 497 PHE 0.011 0.001 PHE A 164 TRP 0.010 0.001 TRP A 530 HIS 0.006 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8552) covalent geometry : angle 0.51464 (11608) hydrogen bonds : bond 0.03774 ( 290) hydrogen bonds : angle 5.57633 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.248 Fit side-chains REVERT: B 369 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8011 (mmtp) REVERT: B 401 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8269 (mmtt) outliers start: 23 outliers final: 20 residues processed: 247 average time/residue: 0.6550 time to fit residues: 170.1455 Evaluate side-chains 252 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 482 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 82 ASN B 327 ASN B 333 ASN B 348 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.112906 restraints weight = 10121.763| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.13 r_work: 0.3593 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8552 Z= 0.238 Angle : 0.548 4.924 11608 Z= 0.296 Chirality : 0.047 0.174 1178 Planarity : 0.005 0.049 1528 Dihedral : 4.726 25.406 1140 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.22 % Allowed : 22.87 % Favored : 73.91 % 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: -0.25 (0.26), residues: 1022 helix: 0.70 (0.68), residues: 68 sheet: 1.06 (0.27), residues: 356 loop : -1.10 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 44 TYR 0.014 0.002 TYR A 190 PHE 0.013 0.002 PHE B 535 TRP 0.010 0.001 TRP A 530 HIS 0.007 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8552) covalent geometry : angle 0.54804 (11608) hydrogen bonds : bond 0.04045 ( 290) hydrogen bonds : angle 5.68235 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.279 Fit side-chains REVERT: B 369 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7999 (mmtp) REVERT: B 401 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8255 (mmtt) outliers start: 28 outliers final: 24 residues processed: 236 average time/residue: 0.5779 time to fit residues: 143.5005 Evaluate side-chains 246 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 96 optimal weight: 0.0670 chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.0670 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 327 ASN B 333 ASN B 348 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114140 restraints weight = 10113.370| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.12 r_work: 0.3615 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 0.029 8552 Z= 0.147 Angle : 0.510 4.858 11608 Z= 0.276 Chirality : 0.044 0.145 1178 Planarity : 0.005 0.053 1528 Dihedral : 4.535 23.116 1140 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.30 % Allowed : 24.25 % Favored : 73.45 % 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: -0.22 (0.26), residues: 1022 helix: 0.84 (0.68), residues: 68 sheet: 0.99 (0.27), residues: 364 loop : -1.06 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 129 TYR 0.010 0.001 TYR B 497 PHE 0.011 0.001 PHE A 164 TRP 0.011 0.001 TRP A 530 HIS 0.007 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8552) covalent geometry : angle 0.50958 (11608) hydrogen bonds : bond 0.03616 ( 290) hydrogen bonds : angle 5.55851 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 171 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7263 (ttp80) REVERT: B 209 GLU cc_start: 0.7192 (tp30) cc_final: 0.6787 (tm-30) REVERT: B 401 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8260 (mmtt) outliers start: 20 outliers final: 15 residues processed: 234 average time/residue: 0.5941 time to fit residues: 145.8454 Evaluate side-chains 237 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.0470 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 35 optimal weight: 0.1980 chunk 101 optimal weight: 0.2980 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114611 restraints weight = 10027.571| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.13 r_work: 0.3621 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8552 Z= 0.133 Angle : 0.508 4.829 11608 Z= 0.275 Chirality : 0.044 0.128 1178 Planarity : 0.005 0.063 1528 Dihedral : 4.453 21.730 1140 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.84 % Allowed : 24.60 % Favored : 73.56 % 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: -0.20 (0.26), residues: 1022 helix: 0.91 (0.68), residues: 68 sheet: 0.93 (0.27), residues: 368 loop : -1.01 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 129 TYR 0.010 0.001 TYR A 518 PHE 0.011 0.001 PHE B 164 TRP 0.010 0.001 TRP A 414 HIS 0.007 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8552) covalent geometry : angle 0.50814 (11608) hydrogen bonds : bond 0.03506 ( 290) hydrogen bonds : angle 5.48742 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7196 (tp30) cc_final: 0.6794 (tm-30) REVERT: B 401 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8262 (mmtt) outliers start: 16 outliers final: 14 residues processed: 234 average time/residue: 0.5570 time to fit residues: 137.3217 Evaluate side-chains 241 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 401 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.0040 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 0.0060 chunk 68 optimal weight: 0.0010 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 overall best weight: 0.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117514 restraints weight = 10200.118| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.15 r_work: 0.3662 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8552 Z= 0.089 Angle : 0.479 4.740 11608 Z= 0.258 Chirality : 0.043 0.136 1178 Planarity : 0.005 0.050 1528 Dihedral : 4.068 17.934 1140 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.26 % Allowed : 25.29 % Favored : 73.45 % 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: -0.14 (0.26), residues: 1022 helix: 1.08 (0.67), residues: 68 sheet: 0.87 (0.27), residues: 374 loop : -0.92 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 129 TYR 0.010 0.001 TYR A 518 PHE 0.014 0.001 PHE A 164 TRP 0.012 0.001 TRP B 530 HIS 0.006 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 8552) covalent geometry : angle 0.47931 (11608) hydrogen bonds : bond 0.02987 ( 290) hydrogen bonds : angle 5.25249 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4310.30 seconds wall clock time: 73 minutes 43.05 seconds (4423.05 seconds total)