Starting phenix.real_space_refine on Sat Aug 23 02:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgx_43229/08_2025/8vgx_43229.cif" } resolution = 2.19 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= 0.002 sd= 0.170 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 14 5.16 5 C 5796 2.51 5 N 1522 2.21 5 O 1802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "B" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' CA': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' CA': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.69, per 1000 atoms: 0.29 Number of scatterers: 9138 At special positions: 0 Unit cell: (106.09, 95.79, 98.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 14 16.00 P 2 15.00 O 1802 8.00 N 1522 7.00 C 5796 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: 0.98 Conformation dependent library (CDL) restraints added in 360.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 51.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.904A pdb=" N TYR A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.851A pdb=" N PHE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.582A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.288A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.771A pdb=" N PHE A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 377 through 402 removed outlier: 4.216A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 532 through 550 Processing helix chain 'A' and resid 554 through 578 removed outlier: 3.658A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.957A pdb=" N TYR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.755A pdb=" N PHE B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 154 through 170 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.865A pdb=" N PHE B 178 " --> pdb=" O PHE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.459A pdb=" N GLU B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.692A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.254A pdb=" N PHE B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.759A pdb=" N PHE B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 377 through 402 removed outlier: 4.191A pdb=" N ALA B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 423 through 426 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 440 through 459 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 532 through 551 Processing helix chain 'B' and resid 554 through 577 Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 5.897A pdb=" N TRP A 125 " --> pdb=" O ASP B 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.716A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.859A pdb=" N VAL A 284 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLY A 318 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.449A pdb=" N LEU A 530 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 586 through 589 Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.963A pdb=" N VAL B 284 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY B 318 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 286 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.546A pdb=" N LEU B 530 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 589 416 hydrogen bonds defined for protein. 1206 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: 1.50 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 3 1.14 - 1.31: 1652 1.31 - 1.47: 3604 1.47 - 1.64: 4043 1.64 - 1.80: 24 Bond restraints: 9326 Sorted by residual: bond pdb=" C HIS B 480 " pdb=" O HIS B 480 " ideal model delta sigma weight residual 1.238 0.978 0.259 1.28e-02 6.10e+03 4.11e+02 bond pdb=" C HIS A 480 " pdb=" O HIS A 480 " ideal model delta sigma weight residual 1.237 1.094 0.143 1.03e-02 9.43e+03 1.93e+02 bond pdb=" CE1 HIS B 480 " pdb=" NE2 HIS B 480 " ideal model delta sigma weight residual 1.321 1.213 0.108 1.00e-02 1.00e+04 1.16e+02 bond pdb=" CG HIS B 480 " pdb=" CD2 HIS B 480 " ideal model delta sigma weight residual 1.354 1.248 0.106 1.10e-02 8.26e+03 9.33e+01 bond pdb=" C GLU A 160 " pdb=" O GLU A 160 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.17e-02 7.31e+03 7.85e+01 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 12637 3.86 - 7.72: 37 7.72 - 11.59: 4 11.59 - 15.45: 0 15.45 - 19.31: 2 Bond angle restraints: 12680 Sorted by residual: angle pdb=" C HIS A 480 " pdb=" CA HIS A 480 " pdb=" CB HIS A 480 " ideal model delta sigma weight residual 109.97 126.13 -16.16 1.55e+00 4.16e-01 1.09e+02 angle pdb=" C HIS B 480 " pdb=" CA HIS B 480 " pdb=" CB HIS B 480 " ideal model delta sigma weight residual 110.17 129.48 -19.31 1.97e+00 2.58e-01 9.61e+01 angle pdb=" CA HIS B 480 " pdb=" C HIS B 480 " pdb=" O HIS B 480 " ideal model delta sigma weight residual 120.16 109.11 11.05 1.37e+00 5.33e-01 6.51e+01 angle pdb=" O HIS B 480 " pdb=" C HIS B 480 " pdb=" N PRO B 481 " ideal model delta sigma weight residual 121.32 130.33 -9.01 1.15e+00 7.56e-01 6.14e+01 angle pdb=" CA HIS B 480 " pdb=" CB HIS B 480 " pdb=" CG HIS B 480 " ideal model delta sigma weight residual 113.80 119.90 -6.10 1.00e+00 1.00e+00 3.72e+01 ... (remaining 12675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4817 17.53 - 35.07: 577 35.07 - 52.60: 136 52.60 - 70.14: 39 70.14 - 87.67: 23 Dihedral angle restraints: 5592 sinusoidal: 2212 harmonic: 3380 Sorted by residual: dihedral pdb=" C HIS B 480 " pdb=" N HIS B 480 " pdb=" CA HIS B 480 " pdb=" CB HIS B 480 " ideal model delta harmonic sigma weight residual -122.60 -149.11 26.51 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N HIS B 480 " pdb=" C HIS B 480 " pdb=" CA HIS B 480 " pdb=" CB HIS B 480 " ideal model delta harmonic sigma weight residual 122.80 141.45 -18.65 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C HIS A 480 " pdb=" N HIS A 480 " pdb=" CA HIS A 480 " pdb=" CB HIS A 480 " ideal model delta harmonic sigma weight residual -122.60 -136.75 14.15 0 2.50e+00 1.60e-01 3.21e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 1401 0.202 - 0.405: 2 0.405 - 0.607: 0 0.607 - 0.810: 0 0.810 - 1.012: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA HIS B 480 " pdb=" N HIS B 480 " pdb=" C HIS B 480 " pdb=" CB HIS B 480 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA HIS A 480 " pdb=" N HIS A 480 " pdb=" C HIS A 480 " pdb=" CB HIS A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CG LEU A 440 " pdb=" CB LEU A 440 " pdb=" CD1 LEU A 440 " pdb=" CD2 LEU A 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1401 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 479 " 0.026 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C PHE B 479 " -0.094 2.00e-02 2.50e+03 pdb=" O PHE B 479 " 0.036 2.00e-02 2.50e+03 pdb=" N HIS B 480 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 341 " 0.022 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C TYR B 341 " -0.081 2.00e-02 2.50e+03 pdb=" O TYR B 341 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 342 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 340 " 0.023 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C ALA B 340 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA B 340 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 341 " 0.026 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1683 2.76 - 3.29: 9879 3.29 - 3.83: 19134 3.83 - 4.36: 22758 4.36 - 4.90: 35269 Nonbonded interactions: 88723 Sorted by model distance: nonbonded pdb=" O LEU A 166 " pdb=" OH TYR A 186 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 412 " pdb=" OH TYR A 554 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 233 " pdb=" OD2 ASP A 541 " model vdw 2.224 3.040 nonbonded pdb=" O PHE A 226 " pdb=" OH TYR A 238 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP A 368 " pdb="CA CA A 601 " model vdw 2.238 2.510 ... (remaining 88718 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' } 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: 16.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.007 0.259 9326 Z= 0.467 Angle : 0.687 19.310 12680 Z= 0.406 Chirality : 0.050 1.012 1404 Planarity : 0.005 0.108 1704 Dihedral : 17.384 87.673 3416 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 19.65 % Favored : 78.29 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.12 (0.24), residues: 1176 helix: 1.07 (0.22), residues: 528 sheet: -0.16 (1.39), residues: 18 loop : 0.66 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.038 0.004 TYR B 238 PHE 0.020 0.002 PHE B 479 TRP 0.008 0.002 TRP B 125 HIS 0.032 0.002 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 9326) covalent geometry : angle 0.68720 (12680) hydrogen bonds : bond 0.13261 ( 416) hydrogen bonds : angle 6.25958 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 90 LYS cc_start: 0.7940 (tptm) cc_final: 0.7319 (tmmm) outliers start: 20 outliers final: 17 residues processed: 138 average time/residue: 0.6125 time to fit residues: 90.0372 Evaluate side-chains 132 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN B 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126838 restraints weight = 9334.261| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.38 r_work: 0.3370 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9326 Z= 0.164 Angle : 0.529 6.254 12680 Z= 0.278 Chirality : 0.040 0.133 1404 Planarity : 0.004 0.074 1704 Dihedral : 6.507 76.441 1283 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.21 % Favored : 97.62 % Rotamer: Outliers : 4.42 % Allowed : 17.70 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.26 (0.25), residues: 1176 helix: 1.16 (0.22), residues: 530 sheet: -0.41 (1.36), residues: 18 loop : 0.78 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 405 TYR 0.029 0.002 TYR A 341 PHE 0.019 0.001 PHE B 479 TRP 0.009 0.002 TRP B 331 HIS 0.005 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9326) covalent geometry : angle 0.52882 (12680) hydrogen bonds : bond 0.04807 ( 416) hydrogen bonds : angle 5.33090 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6797 (p0) cc_final: 0.6283 (m-30) REVERT: A 107 LEU cc_start: 0.8727 (mt) cc_final: 0.8452 (mm) REVERT: A 119 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 171 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8116 (mtt180) REVERT: A 219 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: B 90 LYS cc_start: 0.7919 (tptm) cc_final: 0.7024 (tmmm) REVERT: B 316 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7342 (mp0) REVERT: B 341 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: B 448 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 479 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: B 595 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8213 (t) outliers start: 43 outliers final: 15 residues processed: 163 average time/residue: 0.5997 time to fit residues: 104.0228 Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN B 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127631 restraints weight = 9337.726| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.37 r_work: 0.3381 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9326 Z= 0.154 Angle : 0.519 6.983 12680 Z= 0.271 Chirality : 0.040 0.246 1404 Planarity : 0.004 0.062 1704 Dihedral : 6.077 75.355 1275 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 4.01 % Allowed : 18.00 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.33 (0.25), residues: 1176 helix: 1.19 (0.22), residues: 530 sheet: -0.42 (1.37), residues: 18 loop : 0.84 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 19 TYR 0.026 0.003 TYR A 341 PHE 0.018 0.001 PHE B 479 TRP 0.011 0.002 TRP B 331 HIS 0.003 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9326) covalent geometry : angle 0.51857 (12680) hydrogen bonds : bond 0.04608 ( 416) hydrogen bonds : angle 5.20492 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7082 (t0) cc_final: 0.6878 (t0) REVERT: A 49 ASP cc_start: 0.6800 (p0) cc_final: 0.6264 (m-30) REVERT: A 107 LEU cc_start: 0.8771 (mt) cc_final: 0.8514 (mm) REVERT: A 119 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7582 (mp0) REVERT: A 219 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: A 335 ASP cc_start: 0.7491 (p0) cc_final: 0.7258 (p0) REVERT: A 434 ASP cc_start: 0.7874 (m-30) cc_final: 0.7535 (m-30) REVERT: A 479 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: B 89 GLU cc_start: 0.7188 (mp0) cc_final: 0.6982 (mt-10) REVERT: B 90 LYS cc_start: 0.8100 (tptm) cc_final: 0.7093 (tmmm) REVERT: B 107 LEU cc_start: 0.8533 (mt) cc_final: 0.8171 (mt) REVERT: B 119 GLU cc_start: 0.8106 (mp0) cc_final: 0.7820 (mp0) REVERT: B 479 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.6975 (m-10) REVERT: B 595 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8147 (t) outliers start: 39 outliers final: 15 residues processed: 167 average time/residue: 0.5852 time to fit residues: 104.2651 Evaluate side-chains 130 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 587 ASN B 264 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122747 restraints weight = 9209.867| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.40 r_work: 0.3315 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9326 Z= 0.215 Angle : 0.568 7.680 12680 Z= 0.297 Chirality : 0.042 0.280 1404 Planarity : 0.004 0.057 1704 Dihedral : 6.279 75.200 1273 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 4.32 % Allowed : 18.21 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.24 (0.25), residues: 1176 helix: 1.07 (0.22), residues: 530 sheet: -0.53 (1.35), residues: 18 loop : 0.84 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.029 0.003 TYR A 341 PHE 0.022 0.002 PHE B 479 TRP 0.010 0.002 TRP B 331 HIS 0.003 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9326) covalent geometry : angle 0.56767 (12680) hydrogen bonds : bond 0.05116 ( 416) hydrogen bonds : angle 5.34791 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8801 (mt) cc_final: 0.8521 (mm) REVERT: A 119 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7631 (mp0) REVERT: A 219 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 335 ASP cc_start: 0.7586 (p0) cc_final: 0.7328 (p0) REVERT: A 434 ASP cc_start: 0.7862 (m-30) cc_final: 0.7530 (m-30) REVERT: B 90 LYS cc_start: 0.8134 (tptm) cc_final: 0.7203 (tmmm) REVERT: B 107 LEU cc_start: 0.8614 (mt) cc_final: 0.8263 (mt) REVERT: B 137 GLU cc_start: 0.6396 (tt0) cc_final: 0.5969 (tp30) REVERT: B 163 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7197 (pp20) REVERT: B 448 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 479 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7245 (m-10) outliers start: 42 outliers final: 25 residues processed: 157 average time/residue: 0.6046 time to fit residues: 101.1507 Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 576 GLN B 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125099 restraints weight = 9184.840| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.40 r_work: 0.3344 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9326 Z= 0.179 Angle : 0.543 7.951 12680 Z= 0.283 Chirality : 0.041 0.273 1404 Planarity : 0.004 0.054 1704 Dihedral : 6.193 75.231 1273 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 4.42 % Allowed : 18.52 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1176 helix: 1.07 (0.22), residues: 530 sheet: -0.54 (1.38), residues: 18 loop : 0.79 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.027 0.003 TYR A 341 PHE 0.019 0.001 PHE B 479 TRP 0.014 0.002 TRP B 331 HIS 0.003 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9326) covalent geometry : angle 0.54323 (12680) hydrogen bonds : bond 0.04803 ( 416) hydrogen bonds : angle 5.26534 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6651 (p0) cc_final: 0.6168 (m-30) REVERT: A 107 LEU cc_start: 0.8793 (mt) cc_final: 0.8520 (mm) REVERT: A 119 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 219 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 434 ASP cc_start: 0.7900 (m-30) cc_final: 0.7590 (m-30) REVERT: B 107 LEU cc_start: 0.8616 (mt) cc_final: 0.8270 (mt) REVERT: B 163 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: B 448 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 479 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7082 (m-10) outliers start: 43 outliers final: 22 residues processed: 163 average time/residue: 0.5936 time to fit residues: 102.9456 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 510 GLN A 576 GLN B 264 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128000 restraints weight = 9405.773| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.41 r_work: 0.3392 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9326 Z= 0.144 Angle : 0.518 7.228 12680 Z= 0.267 Chirality : 0.040 0.311 1404 Planarity : 0.004 0.052 1704 Dihedral : 6.007 75.170 1273 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 3.91 % Allowed : 19.03 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.30 (0.25), residues: 1176 helix: 1.17 (0.22), residues: 530 sheet: -0.52 (1.42), residues: 18 loop : 0.82 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.028 0.003 TYR A 341 PHE 0.016 0.001 PHE B 479 TRP 0.018 0.002 TRP B 331 HIS 0.003 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9326) covalent geometry : angle 0.51775 (12680) hydrogen bonds : bond 0.04424 ( 416) hydrogen bonds : angle 5.12583 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6779 (p0) cc_final: 0.6277 (m-30) REVERT: A 119 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7596 (mp0) REVERT: A 219 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: A 335 ASP cc_start: 0.7555 (p0) cc_final: 0.7280 (p0) REVERT: A 387 GLU cc_start: 0.7620 (pt0) cc_final: 0.7328 (tm-30) REVERT: A 434 ASP cc_start: 0.7728 (m-30) cc_final: 0.7303 (m-30) REVERT: B 90 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7639 (tptm) REVERT: B 107 LEU cc_start: 0.8621 (mt) cc_final: 0.8285 (mt) REVERT: B 163 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7164 (pp20) REVERT: B 316 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 371 ASP cc_start: 0.7872 (m-30) cc_final: 0.7638 (m-30) REVERT: B 479 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: B 595 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (t) outliers start: 38 outliers final: 19 residues processed: 165 average time/residue: 0.5472 time to fit residues: 96.7539 Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 576 GLN B 68 ASN B 264 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129221 restraints weight = 9383.618| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.39 r_work: 0.3402 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9326 Z= 0.145 Angle : 0.525 7.516 12680 Z= 0.270 Chirality : 0.041 0.274 1404 Planarity : 0.004 0.050 1704 Dihedral : 5.957 74.796 1273 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 3.81 % Allowed : 19.24 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.26 (0.25), residues: 1176 helix: 1.13 (0.22), residues: 532 sheet: -0.50 (1.43), residues: 18 loop : 0.81 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 391 TYR 0.032 0.003 TYR A 341 PHE 0.023 0.001 PHE B 559 TRP 0.013 0.002 TRP A 331 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9326) covalent geometry : angle 0.52481 (12680) hydrogen bonds : bond 0.04421 ( 416) hydrogen bonds : angle 5.10209 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6737 (p0) cc_final: 0.6251 (m-30) REVERT: A 107 LEU cc_start: 0.8692 (mt) cc_final: 0.8388 (mm) REVERT: A 119 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7540 (mp0) REVERT: A 219 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: A 434 ASP cc_start: 0.7510 (m-30) cc_final: 0.7093 (m-30) REVERT: A 507 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6209 (mt-10) REVERT: B 90 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7592 (tptm) REVERT: B 107 LEU cc_start: 0.8612 (mt) cc_final: 0.8274 (mt) REVERT: B 163 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7112 (pp20) REVERT: B 316 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 341 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: B 371 ASP cc_start: 0.7982 (m-30) cc_final: 0.7689 (m-30) REVERT: B 448 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 479 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: B 595 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (t) outliers start: 37 outliers final: 18 residues processed: 161 average time/residue: 0.5627 time to fit residues: 96.5521 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 510 GLN A 576 GLN B 264 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125659 restraints weight = 9305.347| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.39 r_work: 0.3355 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9326 Z= 0.184 Angle : 0.564 7.989 12680 Z= 0.291 Chirality : 0.042 0.297 1404 Planarity : 0.004 0.049 1704 Dihedral : 6.105 74.409 1273 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 4.01 % Allowed : 19.24 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.19 (0.25), residues: 1176 helix: 1.01 (0.22), residues: 532 sheet: -0.48 (1.42), residues: 18 loop : 0.84 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 391 TYR 0.035 0.003 TYR A 341 PHE 0.021 0.002 PHE B 559 TRP 0.017 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9326) covalent geometry : angle 0.56401 (12680) hydrogen bonds : bond 0.04810 ( 416) hydrogen bonds : angle 5.22533 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8722 (mt) cc_final: 0.8429 (mm) REVERT: A 119 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7564 (mp0) REVERT: A 163 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: A 219 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: A 387 GLU cc_start: 0.7569 (pt0) cc_final: 0.7256 (tm-30) REVERT: A 434 ASP cc_start: 0.7525 (m-30) cc_final: 0.7161 (m-30) REVERT: A 507 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6296 (mt-10) REVERT: B 89 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6826 (mp0) REVERT: B 90 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7602 (tptm) REVERT: B 107 LEU cc_start: 0.8653 (mt) cc_final: 0.8292 (mt) REVERT: B 163 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: B 172 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: B 371 ASP cc_start: 0.7971 (m-30) cc_final: 0.7686 (m-30) REVERT: B 448 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: B 479 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7062 (m-10) REVERT: B 526 PHE cc_start: 0.7266 (t80) cc_final: 0.7012 (t80) REVERT: B 574 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7486 (mt-10) outliers start: 39 outliers final: 24 residues processed: 149 average time/residue: 0.5885 time to fit residues: 93.3327 Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 375 ASN A 510 GLN A 576 GLN B 264 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126177 restraints weight = 9353.165| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.39 r_work: 0.3369 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9326 Z= 0.169 Angle : 0.555 8.200 12680 Z= 0.286 Chirality : 0.041 0.272 1404 Planarity : 0.004 0.049 1704 Dihedral : 6.064 75.012 1273 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 3.91 % Allowed : 19.44 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.20 (0.25), residues: 1176 helix: 1.02 (0.22), residues: 532 sheet: -0.54 (1.43), residues: 18 loop : 0.84 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 397 TYR 0.033 0.003 TYR A 341 PHE 0.019 0.001 PHE B 559 TRP 0.016 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9326) covalent geometry : angle 0.55524 (12680) hydrogen bonds : bond 0.04655 ( 416) hydrogen bonds : angle 5.20893 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6635 (p0) cc_final: 0.6158 (m-30) REVERT: A 107 LEU cc_start: 0.8766 (mt) cc_final: 0.8460 (mm) REVERT: A 119 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7610 (mp0) REVERT: A 163 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7278 (pp20) REVERT: A 188 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: A 219 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 387 GLU cc_start: 0.7560 (pt0) cc_final: 0.7278 (tm-30) REVERT: A 434 ASP cc_start: 0.7422 (m-30) cc_final: 0.7175 (m-30) REVERT: A 507 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: B 90 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7600 (tptm) REVERT: B 107 LEU cc_start: 0.8670 (mt) cc_final: 0.8313 (mt) REVERT: B 163 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: B 172 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 316 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 341 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 371 ASP cc_start: 0.7991 (m-30) cc_final: 0.7714 (m-30) REVERT: B 448 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: B 479 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: B 526 PHE cc_start: 0.7228 (t80) cc_final: 0.6953 (t80) REVERT: B 574 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7495 (mt-10) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.5779 time to fit residues: 93.1407 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 375 ASN A 510 GLN A 576 GLN B 264 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128328 restraints weight = 9299.328| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.42 r_work: 0.3395 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9326 Z= 0.148 Angle : 0.544 8.364 12680 Z= 0.280 Chirality : 0.041 0.253 1404 Planarity : 0.004 0.049 1704 Dihedral : 5.977 74.961 1273 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 3.29 % Allowed : 20.37 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 1.19 (0.25), residues: 1176 helix: 0.99 (0.22), residues: 532 sheet: -0.58 (1.44), residues: 18 loop : 0.86 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 397 TYR 0.034 0.003 TYR A 341 PHE 0.019 0.001 PHE B 559 TRP 0.031 0.003 TRP B 331 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9326) covalent geometry : angle 0.54355 (12680) hydrogen bonds : bond 0.04461 ( 416) hydrogen bonds : angle 5.16789 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6626 (p0) cc_final: 0.6153 (m-30) REVERT: A 107 LEU cc_start: 0.8762 (mt) cc_final: 0.8463 (mm) REVERT: A 119 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7566 (mp0) REVERT: A 219 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: A 335 ASP cc_start: 0.7572 (p0) cc_final: 0.7301 (p0) REVERT: A 387 GLU cc_start: 0.7532 (pt0) cc_final: 0.7244 (tm-30) REVERT: A 434 ASP cc_start: 0.7439 (m-30) cc_final: 0.7183 (m-30) REVERT: B 90 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7602 (tptm) REVERT: B 107 LEU cc_start: 0.8660 (mt) cc_final: 0.8300 (mt) REVERT: B 163 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: B 316 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 371 ASP cc_start: 0.7967 (m-30) cc_final: 0.7669 (m-30) REVERT: B 479 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: B 526 PHE cc_start: 0.7110 (t80) cc_final: 0.6877 (t80) REVERT: B 574 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 595 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8160 (t) outliers start: 32 outliers final: 20 residues processed: 145 average time/residue: 0.6157 time to fit residues: 95.4596 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 67 optimal weight: 0.0770 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 375 ASN A 510 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129100 restraints weight = 9180.375| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.39 r_work: 0.3399 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 9326 Z= 0.182 Angle : 0.883 58.971 12680 Z= 0.523 Chirality : 0.042 0.510 1404 Planarity : 0.004 0.049 1704 Dihedral : 6.065 74.957 1272 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.67 % Allowed : 20.88 % Favored : 76.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.18 (0.25), residues: 1176 helix: 1.00 (0.22), residues: 532 sheet: -0.60 (1.44), residues: 18 loop : 0.83 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.032 0.003 TYR A 341 PHE 0.018 0.001 PHE B 559 TRP 0.029 0.003 TRP B 331 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9326) covalent geometry : angle 0.88299 (12680) hydrogen bonds : bond 0.04462 ( 416) hydrogen bonds : angle 5.16791 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.87 seconds wall clock time: 69 minutes 8.54 seconds (4148.54 seconds total)