Starting phenix.real_space_refine on Sun Jul 27 07:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgx_43229/07_2025/8vgx_43229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgx_43229/07_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_43229/07_2025/8vgx_43229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgx_43229/07_2025/8vgx_43229.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgx_43229/07_2025/8vgx_43229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgx_43229/07_2025/8vgx_43229.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.13, per 1000 atoms: 0.89 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.42 Time building geometry restraints manager: 2.96 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: 0.04 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: 149.440 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.640 ------------------------------------------------------------------------------- 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 : 14.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP B 125 HIS 0.032 0.002 HIS B 480 PHE 0.020 0.002 PHE B 479 TYR 0.038 0.004 TYR B 238 ARG 0.003 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.13261 ( 416) hydrogen bonds : angle 6.25958 ( 1206) covalent geometry : bond 0.00678 ( 9326) covalent geometry : angle 0.68720 (12680) *********************** 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 : 1.204 Fit side-chains 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: 1.3070 time to fit residues: 192.9619 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 : 1.033 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN B 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124015 restraints weight = 9297.735| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.39 r_work: 0.3341 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9326 Z= 0.188 Angle : 0.547 6.555 12680 Z= 0.288 Chirality : 0.041 0.136 1404 Planarity : 0.004 0.074 1704 Dihedral : 6.599 76.127 1283 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 4.42 % Allowed : 18.00 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1176 helix: 1.11 (0.22), residues: 530 sheet: -0.39 (1.37), residues: 18 loop : 0.77 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 125 HIS 0.006 0.001 HIS B 480 PHE 0.022 0.002 PHE B 479 TYR 0.029 0.003 TYR A 341 ARG 0.004 0.001 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 416) hydrogen bonds : angle 5.38463 ( 1206) covalent geometry : bond 0.00419 ( 9326) covalent geometry : angle 0.54727 (12680) *********************** 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 : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8763 (mt) cc_final: 0.8492 (mm) REVERT: A 119 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7565 (mp0) REVERT: A 171 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8227 (mtt180) REVERT: A 219 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 90 LYS cc_start: 0.7925 (tptm) cc_final: 0.6998 (tmmm) REVERT: B 341 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: B 448 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: B 479 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7257 (m-10) outliers start: 43 outliers final: 16 residues processed: 161 average time/residue: 1.5044 time to fit residues: 259.6394 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 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 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 86 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125263 restraints weight = 9391.836| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.39 r_work: 0.3349 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9326 Z= 0.175 Angle : 0.537 6.997 12680 Z= 0.281 Chirality : 0.041 0.234 1404 Planarity : 0.004 0.063 1704 Dihedral : 6.376 75.413 1277 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 4.12 % Allowed : 17.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1176 helix: 1.13 (0.22), residues: 530 sheet: -0.43 (1.39), residues: 18 loop : 0.81 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 331 HIS 0.003 0.001 HIS B 480 PHE 0.021 0.001 PHE B 479 TYR 0.026 0.003 TYR A 341 ARG 0.005 0.001 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 416) hydrogen bonds : angle 5.27828 ( 1206) covalent geometry : bond 0.00390 ( 9326) covalent geometry : angle 0.53654 (12680) *********************** 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: 40 poor density : 134 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8775 (mt) cc_final: 0.8493 (mm) REVERT: A 119 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7574 (mp0) REVERT: A 219 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 90 LYS cc_start: 0.8051 (tptm) cc_final: 0.7119 (tmmm) REVERT: B 163 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: B 448 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 479 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7165 (m-10) outliers start: 40 outliers final: 17 residues processed: 164 average time/residue: 1.8173 time to fit residues: 317.4163 Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 A 587 ASN B 264 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121284 restraints weight = 9239.795| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.38 r_work: 0.3298 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 9326 Z= 0.241 Angle : 0.590 7.861 12680 Z= 0.310 Chirality : 0.043 0.296 1404 Planarity : 0.004 0.058 1704 Dihedral : 6.435 75.849 1274 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.38 % Favored : 97.45 % Rotamer: Outliers : 4.73 % Allowed : 18.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1176 helix: 1.01 (0.22), residues: 530 sheet: -0.46 (1.40), residues: 18 loop : 0.77 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 331 HIS 0.003 0.001 HIS A 480 PHE 0.024 0.002 PHE B 479 TYR 0.028 0.003 TYR A 341 ARG 0.005 0.001 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 416) hydrogen bonds : angle 5.40480 ( 1206) covalent geometry : bond 0.00539 ( 9326) covalent geometry : angle 0.58986 (12680) *********************** 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 173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8780 (mt) cc_final: 0.8490 (mm) REVERT: A 119 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7575 (mp0) REVERT: A 219 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 434 ASP cc_start: 0.7908 (m-30) cc_final: 0.7573 (m-30) REVERT: B 90 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7149 (tmmm) REVERT: B 163 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: B 438 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: B 448 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 479 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.7292 (m-10) outliers start: 46 outliers final: 22 residues processed: 159 average time/residue: 1.3268 time to fit residues: 224.9893 Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 128 SER 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 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 180 SER Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 296 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125733 restraints weight = 9176.503| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.40 r_work: 0.3353 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9326 Z= 0.166 Angle : 0.534 7.528 12680 Z= 0.278 Chirality : 0.041 0.269 1404 Planarity : 0.004 0.054 1704 Dihedral : 6.231 75.669 1274 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 4.32 % Allowed : 18.31 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1176 helix: 1.08 (0.22), residues: 530 sheet: -0.42 (1.42), residues: 18 loop : 0.77 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 331 HIS 0.003 0.001 HIS A 480 PHE 0.018 0.001 PHE B 479 TYR 0.026 0.003 TYR B 341 ARG 0.003 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 416) hydrogen bonds : angle 5.24695 ( 1206) covalent geometry : bond 0.00369 ( 9326) covalent geometry : angle 0.53355 (12680) *********************** 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: 42 poor density : 131 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6687 (p0) cc_final: 0.6123 (m-30) REVERT: A 90 LYS cc_start: 0.7807 (tttt) cc_final: 0.7544 (tttp) REVERT: A 107 LEU cc_start: 0.8857 (mt) cc_final: 0.8592 (mm) REVERT: A 119 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7614 (mp0) REVERT: A 219 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: A 335 ASP cc_start: 0.7480 (p0) cc_final: 0.7252 (p0) REVERT: A 387 GLU cc_start: 0.7617 (pt0) cc_final: 0.7341 (tm-30) REVERT: A 434 ASP cc_start: 0.7829 (m-30) cc_final: 0.7512 (m-30) REVERT: B 119 GLU cc_start: 0.8146 (mp0) cc_final: 0.7894 (mp0) REVERT: B 163 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: B 341 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 479 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7089 (m-10) outliers start: 42 outliers final: 18 residues processed: 163 average time/residue: 1.2637 time to fit residues: 219.8850 Evaluate side-chains 132 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 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 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 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124835 restraints weight = 9307.183| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.40 r_work: 0.3352 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9326 Z= 0.172 Angle : 0.540 7.475 12680 Z= 0.280 Chirality : 0.041 0.324 1404 Planarity : 0.004 0.053 1704 Dihedral : 6.178 75.148 1274 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.21 % Favored : 97.62 % Rotamer: Outliers : 4.32 % Allowed : 18.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1176 helix: 1.07 (0.22), residues: 530 sheet: -0.42 (1.43), residues: 18 loop : 0.79 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 331 HIS 0.003 0.001 HIS A 404 PHE 0.019 0.001 PHE B 479 TYR 0.028 0.003 TYR A 341 ARG 0.004 0.001 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 416) hydrogen bonds : angle 5.23357 ( 1206) covalent geometry : bond 0.00383 ( 9326) covalent geometry : angle 0.54038 (12680) *********************** 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 168 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6638 (p0) cc_final: 0.6161 (m-30) REVERT: A 90 LYS cc_start: 0.7862 (tttt) cc_final: 0.7608 (tttp) REVERT: A 107 LEU cc_start: 0.8857 (mt) cc_final: 0.8592 (mm) REVERT: A 119 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7605 (mp0) REVERT: A 219 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: A 434 ASP cc_start: 0.7852 (m-30) cc_final: 0.7440 (m-30) REVERT: A 595 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 89 GLU cc_start: 0.7296 (mp0) cc_final: 0.7090 (mt-10) REVERT: B 90 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7646 (tptm) REVERT: B 107 LEU cc_start: 0.8550 (mt) cc_final: 0.8198 (mt) REVERT: B 163 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: B 448 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 479 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7117 (m-10) outliers start: 42 outliers final: 23 residues processed: 159 average time/residue: 1.3228 time to fit residues: 224.4552 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 A residue 595 THR 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 235 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 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 188 GLN A 264 ASN A 510 GLN A 576 GLN B 68 ASN B 188 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126381 restraints weight = 9411.089| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.40 r_work: 0.3372 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9326 Z= 0.157 Angle : 0.537 7.785 12680 Z= 0.277 Chirality : 0.041 0.284 1404 Planarity : 0.004 0.051 1704 Dihedral : 6.115 75.029 1274 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.21 % Favored : 97.62 % Rotamer: Outliers : 4.32 % Allowed : 18.52 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1176 helix: 1.05 (0.22), residues: 532 sheet: -0.48 (1.43), residues: 18 loop : 0.79 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 PHE 0.017 0.001 PHE B 479 TYR 0.027 0.003 TYR A 341 ARG 0.005 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 416) hydrogen bonds : angle 5.20019 ( 1206) covalent geometry : bond 0.00348 ( 9326) covalent geometry : angle 0.53680 (12680) *********************** 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 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6607 (p0) cc_final: 0.6129 (m-30) REVERT: A 107 LEU cc_start: 0.8892 (mt) cc_final: 0.8638 (mm) REVERT: A 119 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 163 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: A 219 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 434 ASP cc_start: 0.7532 (m-30) cc_final: 0.7180 (m-30) REVERT: A 595 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8038 (t) REVERT: B 90 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7677 (tptm) REVERT: B 107 LEU cc_start: 0.8594 (mt) cc_final: 0.8241 (mt) REVERT: B 163 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: B 316 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 341 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: B 448 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 479 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: B 595 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (t) outliers start: 42 outliers final: 19 residues processed: 157 average time/residue: 1.2876 time to fit residues: 215.9360 Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 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 A residue 595 THR 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 235 VAL 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 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 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 188 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 = 0.3738 r_free = 0.3738 target = 0.148023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126948 restraints weight = 9404.948| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.42 r_work: 0.3370 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9326 Z= 0.162 Angle : 0.545 7.999 12680 Z= 0.280 Chirality : 0.041 0.249 1404 Planarity : 0.004 0.050 1704 Dihedral : 6.099 74.941 1274 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.62 % Rotamer: Outliers : 3.81 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1176 helix: 1.05 (0.22), residues: 532 sheet: -0.52 (1.45), residues: 18 loop : 0.83 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 PHE 0.017 0.001 PHE B 479 TYR 0.031 0.003 TYR A 341 ARG 0.005 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 416) hydrogen bonds : angle 5.19876 ( 1206) covalent geometry : bond 0.00359 ( 9326) covalent geometry : angle 0.54454 (12680) *********************** 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 154 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6612 (p0) cc_final: 0.6131 (m-30) REVERT: A 107 LEU cc_start: 0.8888 (mt) cc_final: 0.8635 (mm) REVERT: A 119 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7650 (mp0) REVERT: A 219 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 387 GLU cc_start: 0.7581 (pt0) cc_final: 0.7290 (tm-30) REVERT: A 434 ASP cc_start: 0.7553 (m-30) cc_final: 0.7177 (m-30) REVERT: A 507 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6264 (mt-10) REVERT: A 595 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 89 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6844 (mp0) REVERT: B 90 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7631 (tptm) REVERT: B 107 LEU cc_start: 0.8629 (mt) cc_final: 0.8272 (mt) REVERT: B 163 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: B 316 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 371 ASP cc_start: 0.7991 (m-30) cc_final: 0.7736 (m-30) REVERT: B 448 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: B 479 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: B 595 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8202 (t) outliers start: 37 outliers final: 22 residues processed: 146 average time/residue: 1.5232 time to fit residues: 237.2621 Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 507 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 THR 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 235 VAL 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 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 112 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 188 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 = 0.3743 r_free = 0.3743 target = 0.148457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127563 restraints weight = 9127.538| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.40 r_work: 0.3378 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9326 Z= 0.160 Angle : 0.548 8.221 12680 Z= 0.283 Chirality : 0.041 0.244 1404 Planarity : 0.004 0.050 1704 Dihedral : 6.078 74.845 1274 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 3.81 % Allowed : 20.06 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1176 helix: 1.07 (0.22), residues: 530 sheet: -0.50 (1.46), residues: 18 loop : 0.86 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 PHE 0.027 0.001 PHE B 559 TYR 0.030 0.003 TYR A 341 ARG 0.004 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 416) hydrogen bonds : angle 5.19172 ( 1206) covalent geometry : bond 0.00355 ( 9326) covalent geometry : angle 0.54789 (12680) *********************** 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 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6605 (p0) cc_final: 0.6128 (m-30) REVERT: A 107 LEU cc_start: 0.8881 (mt) cc_final: 0.8644 (mm) REVERT: A 119 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7605 (mp0) REVERT: A 219 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: A 387 GLU cc_start: 0.7573 (pt0) cc_final: 0.7287 (tm-30) REVERT: A 434 ASP cc_start: 0.7400 (m-30) cc_final: 0.7148 (m-30) REVERT: A 595 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8037 (t) REVERT: B 90 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7600 (tptm) REVERT: B 107 LEU cc_start: 0.8632 (mt) cc_final: 0.8276 (mt) REVERT: B 119 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 163 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: B 167 MET cc_start: 0.8640 (mtt) cc_final: 0.8397 (mtt) REVERT: B 316 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 341 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: B 448 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: B 479 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7040 (m-10) REVERT: B 595 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8181 (t) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 1.2868 time to fit residues: 199.5958 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 A residue 595 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 119 GLU 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 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 30 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 B 188 GLN B 304 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123279 restraints weight = 9358.847| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.40 r_work: 0.3322 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9326 Z= 0.216 Angle : 0.598 8.702 12680 Z= 0.310 Chirality : 0.043 0.282 1404 Planarity : 0.005 0.051 1704 Dihedral : 6.326 75.347 1274 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 3.50 % Allowed : 20.99 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1176 helix: 0.93 (0.22), residues: 532 sheet: -0.46 (1.46), residues: 18 loop : 0.81 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 331 HIS 0.007 0.001 HIS B 480 PHE 0.027 0.002 PHE B 559 TYR 0.036 0.003 TYR A 341 ARG 0.005 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 416) hydrogen bonds : angle 5.32431 ( 1206) covalent geometry : bond 0.00482 ( 9326) covalent geometry : angle 0.59783 (12680) ********************** 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 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7833 (tttt) cc_final: 0.7571 (tttp) REVERT: A 107 LEU cc_start: 0.8884 (mt) cc_final: 0.8646 (mm) REVERT: A 119 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7672 (mp0) REVERT: A 163 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: A 219 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 387 GLU cc_start: 0.7565 (pt0) cc_final: 0.7283 (tm-30) REVERT: A 434 ASP cc_start: 0.7527 (m-30) cc_final: 0.7184 (m-30) REVERT: A 507 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: B 90 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7662 (tptm) REVERT: B 107 LEU cc_start: 0.8605 (mt) cc_final: 0.8248 (mt) REVERT: B 119 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 163 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7150 (pp20) REVERT: B 371 ASP cc_start: 0.7905 (m-30) cc_final: 0.7670 (m-30) REVERT: B 448 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: B 479 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: B 526 PHE cc_start: 0.7457 (t80) cc_final: 0.6970 (t80) outliers start: 34 outliers final: 19 residues processed: 142 average time/residue: 1.3415 time to fit residues: 202.8569 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 390 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 173 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 188 GLN ** 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 = 0.3727 r_free = 0.3727 target = 0.147544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126864 restraints weight = 9333.569| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.39 r_work: 0.3377 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9326 Z= 0.162 Angle : 0.557 8.344 12680 Z= 0.287 Chirality : 0.041 0.250 1404 Planarity : 0.004 0.049 1704 Dihedral : 6.177 75.602 1274 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 3.09 % Allowed : 21.09 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1176 helix: 1.01 (0.22), residues: 530 sheet: -0.53 (1.47), residues: 18 loop : 0.84 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 331 HIS 0.007 0.001 HIS B 480 PHE 0.027 0.001 PHE B 559 TYR 0.034 0.003 TYR A 341 ARG 0.005 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 416) hydrogen bonds : angle 5.21168 ( 1206) covalent geometry : bond 0.00359 ( 9326) covalent geometry : angle 0.55663 (12680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9599.46 seconds wall clock time: 170 minutes 24.04 seconds (10224.04 seconds total)