Starting phenix.real_space_refine on Tue Mar 3 15:39:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2026/7p1i_13161.map" } resolution = 3.15 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= 0.006 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4416 2.51 5 N 1074 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3322 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 21, 'TRANS': 420} Chain breaks: 1 Restraints were copied for chains: A Time building chain proxies: 2.31, per 1000 atoms: 0.35 Number of scatterers: 6644 At special positions: 0 Unit cell: (121.388, 102.713, 88.1875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1114 8.00 N 1074 7.00 C 4416 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: 0.70 Conformation dependent library (CDL) restraints added in 316.7 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 83.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 80 through 104 removed outlier: 4.409A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.629A pdb=" N GLY B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.199A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 191 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 200 through 223 Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.206A pdb=" N LEU B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 326 removed outlier: 3.788A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 removed outlier: 3.541A pdb=" N GLY B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 376 removed outlier: 3.893A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 405 removed outlier: 4.284A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 416 through 439 removed outlier: 4.468A pdb=" N CYS B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 460 through 478 removed outlier: 4.045A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 516 removed outlier: 3.603A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 513 - end of helix removed outlier: 3.819A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 80 through 104 removed outlier: 4.410A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.629A pdb=" N GLY A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.199A pdb=" N GLY A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 191 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 200 through 223 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 276 through 293 removed outlier: 4.205A pdb=" N LEU A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 326 removed outlier: 3.787A pdb=" N PHE A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.541A pdb=" N GLY A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 376 removed outlier: 3.892A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.285A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 416 through 439 removed outlier: 4.468A pdb=" N CYS A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.045A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 516 removed outlier: 3.602A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix Proline residue: A 513 - end of helix removed outlier: 3.818A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1527 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: 1.36 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2026 1.34 - 1.46: 1388 1.46 - 1.58: 3316 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6790 Sorted by residual: bond pdb=" N ILE A 323 " pdb=" CA ILE A 323 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.41e-02 5.03e+03 5.66e+00 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.41e-02 5.03e+03 5.46e+00 bond pdb=" N PHE B 321 " pdb=" CA PHE B 321 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.35e-02 5.49e+03 4.07e+00 bond pdb=" N PHE A 321 " pdb=" CA PHE A 321 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.35e-02 5.49e+03 4.05e+00 bond pdb=" N GLN A 324 " pdb=" CA GLN A 324 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.61e+00 ... (remaining 6785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 9061 1.70 - 3.40: 133 3.40 - 5.11: 40 5.11 - 6.81: 8 6.81 - 8.51: 2 Bond angle restraints: 9244 Sorted by residual: angle pdb=" C TRP B 456 " pdb=" N LEU B 457 " pdb=" CA LEU B 457 " ideal model delta sigma weight residual 120.26 125.13 -4.87 1.34e+00 5.57e-01 1.32e+01 angle pdb=" C PHE A 322 " pdb=" CA PHE A 322 " pdb=" CB PHE A 322 " ideal model delta sigma weight residual 110.56 117.20 -6.64 1.83e+00 2.99e-01 1.32e+01 angle pdb=" C PHE B 322 " pdb=" CA PHE B 322 " pdb=" CB PHE B 322 " ideal model delta sigma weight residual 110.56 117.19 -6.63 1.83e+00 2.99e-01 1.31e+01 angle pdb=" C TRP A 456 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " ideal model delta sigma weight residual 120.26 125.11 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C GLN A 324 " pdb=" CA GLN A 324 " pdb=" CB GLN A 324 " ideal model delta sigma weight residual 110.79 105.29 5.50 1.66e+00 3.63e-01 1.10e+01 ... (remaining 9239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 3639 13.80 - 27.61: 207 27.61 - 41.41: 72 41.41 - 55.21: 26 55.21 - 69.02: 8 Dihedral angle restraints: 3952 sinusoidal: 1482 harmonic: 2470 Sorted by residual: dihedral pdb=" CA ILE A 499 " pdb=" C ILE A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CA ILE B 499 " pdb=" C ILE B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" CB ILE A 323 " pdb=" CG1 ILE A 323 " ideal model delta sinusoidal sigma weight residual 60.00 2.08 57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 921 0.048 - 0.096: 193 0.096 - 0.143: 18 0.143 - 0.191: 0 0.191 - 0.239: 4 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE B 323 " pdb=" N ILE B 323 " pdb=" C ILE B 323 " pdb=" CB ILE B 323 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLN B 324 " pdb=" N GLN B 324 " pdb=" C GLN B 324 " pdb=" CB GLN B 324 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1133 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 512 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 513 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 512 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 513 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 136 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 137 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.019 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1519 2.79 - 3.32: 7275 3.32 - 3.85: 11288 3.85 - 4.37: 11385 4.37 - 4.90: 20702 Nonbonded interactions: 52169 Sorted by model distance: nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.265 3.120 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.265 3.120 nonbonded pdb=" OG SER A 353 " pdb=" O PHE A 358 " model vdw 2.345 3.040 nonbonded pdb=" OG SER B 353 " pdb=" O PHE B 358 " model vdw 2.345 3.040 nonbonded pdb=" NH1 ARG B 431 " pdb=" O TRP B 456 " model vdw 2.368 3.120 ... (remaining 52164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.330 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6790 Z= 0.126 Angle : 0.567 8.510 9244 Z= 0.300 Chirality : 0.038 0.239 1136 Planarity : 0.004 0.042 1122 Dihedral : 11.178 69.016 2376 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.90 % Allowed : 7.30 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.31), residues: 876 helix: 3.39 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.49 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 431 TYR 0.004 0.001 TYR A 485 PHE 0.008 0.001 PHE B 322 TRP 0.011 0.001 TRP A 392 HIS 0.001 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6790) covalent geometry : angle 0.56694 ( 9244) hydrogen bonds : bond 0.10103 ( 513) hydrogen bonds : angle 3.99733 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 PHE cc_start: 0.8373 (m-80) cc_final: 0.8048 (m-10) REVERT: B 154 LEU cc_start: 0.9166 (mt) cc_final: 0.8866 (mt) REVERT: B 176 ARG cc_start: 0.8257 (mpp80) cc_final: 0.7922 (mtt-85) REVERT: B 180 LEU cc_start: 0.9684 (tp) cc_final: 0.9461 (tt) REVERT: B 252 MET cc_start: 0.7869 (mmt) cc_final: 0.7522 (mmt) REVERT: B 340 PHE cc_start: 0.9156 (t80) cc_final: 0.8756 (t80) REVERT: B 392 TRP cc_start: 0.8692 (t-100) cc_final: 0.8237 (t-100) REVERT: B 459 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.5823 (mtmt) REVERT: B 472 ASP cc_start: 0.8808 (m-30) cc_final: 0.8355 (m-30) REVERT: A 107 GLU cc_start: 0.7629 (mp0) cc_final: 0.7263 (mp0) REVERT: A 131 PHE cc_start: 0.9175 (m-80) cc_final: 0.8830 (m-80) REVERT: A 154 LEU cc_start: 0.9309 (mt) cc_final: 0.9099 (mt) REVERT: A 225 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 285 PHE cc_start: 0.8579 (t80) cc_final: 0.8281 (t80) REVERT: A 332 ASP cc_start: 0.9155 (m-30) cc_final: 0.8841 (p0) REVERT: A 365 CYS cc_start: 0.9267 (t) cc_final: 0.9023 (t) REVERT: A 372 LEU cc_start: 0.9569 (mm) cc_final: 0.9347 (tt) REVERT: A 385 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8779 (mm-30) REVERT: A 407 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7386 (t) REVERT: A 426 ILE cc_start: 0.9115 (mm) cc_final: 0.8776 (pt) outliers start: 42 outliers final: 10 residues processed: 311 average time/residue: 0.0674 time to fit residues: 29.0670 Evaluate side-chains 216 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 459 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 396 GLN A 89 ASN A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.081085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.071650 restraints weight = 34978.546| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 6.05 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6790 Z= 0.145 Angle : 0.888 15.353 9244 Z= 0.388 Chirality : 0.042 0.218 1136 Planarity : 0.005 0.041 1122 Dihedral : 6.791 65.154 958 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.92 % Allowed : 23.03 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.29), residues: 876 helix: 2.38 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.76 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.017 0.002 TYR B 260 PHE 0.034 0.002 PHE B 234 TRP 0.025 0.001 TRP B 377 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6790) covalent geometry : angle 0.88845 ( 9244) hydrogen bonds : bond 0.04051 ( 513) hydrogen bonds : angle 3.92464 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7752 (mp0) cc_final: 0.7521 (mp0) REVERT: B 154 LEU cc_start: 0.9349 (mt) cc_final: 0.9101 (mt) REVERT: B 176 ARG cc_start: 0.8370 (mpp80) cc_final: 0.8159 (mtt-85) REVERT: B 253 LEU cc_start: 0.9440 (mm) cc_final: 0.9152 (pp) REVERT: B 257 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8763 (mt-10) REVERT: B 311 ILE cc_start: 0.8938 (tt) cc_final: 0.8703 (pt) REVERT: B 392 TRP cc_start: 0.9089 (t-100) cc_final: 0.8726 (t-100) REVERT: B 456 TRP cc_start: 0.7032 (t-100) cc_final: 0.6538 (t-100) REVERT: B 459 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6076 (mtmt) REVERT: B 472 ASP cc_start: 0.8862 (m-30) cc_final: 0.8594 (m-30) REVERT: A 107 GLU cc_start: 0.7746 (mp0) cc_final: 0.7235 (mp0) REVERT: A 123 CYS cc_start: 0.9481 (m) cc_final: 0.9240 (p) REVERT: A 131 PHE cc_start: 0.9003 (m-80) cc_final: 0.8789 (m-10) REVERT: A 154 LEU cc_start: 0.9320 (mt) cc_final: 0.9081 (mt) REVERT: A 225 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6753 (tp) REVERT: A 277 ASP cc_start: 0.8568 (p0) cc_final: 0.8090 (m-30) REVERT: A 285 PHE cc_start: 0.8220 (t80) cc_final: 0.7941 (t80) REVERT: A 331 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: A 332 ASP cc_start: 0.9207 (m-30) cc_final: 0.8734 (p0) REVERT: A 365 CYS cc_start: 0.9100 (t) cc_final: 0.8892 (t) REVERT: A 407 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7359 (p) REVERT: A 456 TRP cc_start: 0.6996 (t-100) cc_final: 0.6712 (t-100) REVERT: A 466 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8958 (tp) outliers start: 35 outliers final: 18 residues processed: 235 average time/residue: 0.0604 time to fit residues: 19.9394 Evaluate side-chains 227 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 396 GLN A 89 ASN A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.080833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.071261 restraints weight = 34994.705| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 5.96 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6790 Z= 0.148 Angle : 0.856 13.833 9244 Z= 0.383 Chirality : 0.044 0.264 1136 Planarity : 0.004 0.043 1122 Dihedral : 6.307 67.242 949 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.18 % Allowed : 21.91 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 876 helix: 2.03 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.75 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.015 0.001 TYR B 260 PHE 0.041 0.002 PHE B 326 TRP 0.011 0.001 TRP A 456 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6790) covalent geometry : angle 0.85559 ( 9244) hydrogen bonds : bond 0.03881 ( 513) hydrogen bonds : angle 4.09008 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7675 (mp0) cc_final: 0.7441 (mp0) REVERT: B 154 LEU cc_start: 0.9351 (mt) cc_final: 0.9135 (mt) REVERT: B 180 LEU cc_start: 0.9676 (tt) cc_final: 0.9183 (pp) REVERT: B 311 ILE cc_start: 0.8803 (tt) cc_final: 0.8577 (pt) REVERT: B 332 ASP cc_start: 0.8555 (p0) cc_final: 0.8336 (p0) REVERT: B 365 CYS cc_start: 0.8864 (t) cc_final: 0.8633 (t) REVERT: B 392 TRP cc_start: 0.9180 (t-100) cc_final: 0.8962 (t-100) REVERT: B 459 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6113 (mtmt) REVERT: B 472 ASP cc_start: 0.8751 (m-30) cc_final: 0.8478 (m-30) REVERT: A 92 MET cc_start: 0.9432 (ptp) cc_final: 0.9173 (ppp) REVERT: A 107 GLU cc_start: 0.7870 (mp0) cc_final: 0.7289 (mp0) REVERT: A 154 LEU cc_start: 0.9325 (mt) cc_final: 0.9079 (mt) REVERT: A 225 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6824 (tp) REVERT: A 285 PHE cc_start: 0.8410 (t80) cc_final: 0.8181 (t80) REVERT: A 407 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 431 ARG cc_start: 0.8605 (ptm160) cc_final: 0.8043 (ptm160) REVERT: A 466 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9093 (tp) REVERT: A 511 LEU cc_start: 0.8033 (tp) cc_final: 0.7787 (tp) outliers start: 44 outliers final: 24 residues processed: 230 average time/residue: 0.0543 time to fit residues: 17.9715 Evaluate side-chains 215 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.120741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.113176 restraints weight = 38913.329| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.67 r_work: 0.3751 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6790 Z= 0.140 Angle : 0.831 13.101 9244 Z= 0.376 Chirality : 0.043 0.199 1136 Planarity : 0.004 0.048 1122 Dihedral : 5.811 52.206 942 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.20 % Allowed : 24.72 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.29), residues: 876 helix: 1.79 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -2.83 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.024 0.002 TYR B 485 PHE 0.045 0.002 PHE B 326 TRP 0.011 0.001 TRP A 377 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6790) covalent geometry : angle 0.83115 ( 9244) hydrogen bonds : bond 0.03783 ( 513) hydrogen bonds : angle 4.16662 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7784 (mp0) cc_final: 0.7567 (mp0) REVERT: B 154 LEU cc_start: 0.9398 (mt) cc_final: 0.9181 (mt) REVERT: B 308 GLU cc_start: 0.8179 (tp30) cc_final: 0.7724 (mm-30) REVERT: B 365 CYS cc_start: 0.9187 (t) cc_final: 0.8889 (t) REVERT: B 367 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 392 TRP cc_start: 0.9271 (t-100) cc_final: 0.9014 (t-100) REVERT: B 456 TRP cc_start: 0.7830 (t-100) cc_final: 0.7450 (t-100) REVERT: B 459 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6073 (mtmt) REVERT: B 472 ASP cc_start: 0.8865 (m-30) cc_final: 0.8582 (m-30) REVERT: A 225 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7528 (tp) REVERT: A 285 PHE cc_start: 0.8735 (t80) cc_final: 0.8534 (t80) REVERT: A 332 ASP cc_start: 0.9388 (m-30) cc_final: 0.8880 (p0) REVERT: A 408 LEU cc_start: 0.8471 (mt) cc_final: 0.8229 (mt) REVERT: A 466 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9113 (tp) outliers start: 37 outliers final: 25 residues processed: 215 average time/residue: 0.0515 time to fit residues: 16.4510 Evaluate side-chains 208 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.081388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.072451 restraints weight = 37562.400| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 5.56 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6790 Z= 0.188 Angle : 0.853 11.222 9244 Z= 0.398 Chirality : 0.044 0.242 1136 Planarity : 0.005 0.044 1122 Dihedral : 5.778 56.872 941 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.60 % Allowed : 25.42 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.29), residues: 876 helix: 1.59 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.87 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 176 TYR 0.043 0.002 TYR B 485 PHE 0.046 0.002 PHE B 326 TRP 0.009 0.001 TRP A 392 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6790) covalent geometry : angle 0.85266 ( 9244) hydrogen bonds : bond 0.03972 ( 513) hydrogen bonds : angle 4.37590 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7743 (mp0) cc_final: 0.7398 (mp0) REVERT: B 154 LEU cc_start: 0.9367 (mt) cc_final: 0.9138 (mt) REVERT: B 240 LEU cc_start: 0.8601 (tp) cc_final: 0.8352 (tp) REVERT: B 252 MET cc_start: 0.8494 (tmm) cc_final: 0.8046 (tmm) REVERT: B 253 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8931 (mm) REVERT: B 311 ILE cc_start: 0.9024 (tt) cc_final: 0.8809 (pt) REVERT: B 367 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9298 (mm) REVERT: B 399 LEU cc_start: 0.9592 (pp) cc_final: 0.9280 (pp) REVERT: B 459 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.5955 (mtmt) REVERT: B 472 ASP cc_start: 0.8795 (m-30) cc_final: 0.8530 (m-30) REVERT: A 157 ASN cc_start: 0.8398 (p0) cc_final: 0.8192 (p0) REVERT: A 225 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6623 (mp) REVERT: A 332 ASP cc_start: 0.9201 (m-30) cc_final: 0.8805 (p0) REVERT: A 466 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9145 (tp) outliers start: 47 outliers final: 32 residues processed: 209 average time/residue: 0.0546 time to fit residues: 16.6094 Evaluate side-chains 215 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 481 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN A 89 ASN A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.070510 restraints weight = 35798.198| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 5.78 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6790 Z= 0.162 Angle : 0.866 13.901 9244 Z= 0.389 Chirality : 0.044 0.216 1136 Planarity : 0.005 0.044 1122 Dihedral : 5.887 59.298 941 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.90 % Allowed : 26.26 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.29), residues: 876 helix: 1.49 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -2.87 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 156 TYR 0.042 0.002 TYR B 485 PHE 0.041 0.002 PHE B 326 TRP 0.033 0.001 TRP B 392 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6790) covalent geometry : angle 0.86581 ( 9244) hydrogen bonds : bond 0.03879 ( 513) hydrogen bonds : angle 4.30549 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7801 (mp0) cc_final: 0.7501 (mp0) REVERT: B 154 LEU cc_start: 0.9355 (mt) cc_final: 0.9122 (mt) REVERT: B 240 LEU cc_start: 0.8536 (tp) cc_final: 0.8309 (tp) REVERT: B 311 ILE cc_start: 0.8918 (tt) cc_final: 0.8687 (pt) REVERT: B 367 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9231 (mm) REVERT: B 456 TRP cc_start: 0.6906 (t-100) cc_final: 0.6651 (t-100) REVERT: B 459 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.5967 (mtmt) REVERT: B 472 ASP cc_start: 0.8824 (m-30) cc_final: 0.8559 (m-30) REVERT: A 92 MET cc_start: 0.9368 (ptt) cc_final: 0.9135 (ppp) REVERT: A 189 LEU cc_start: 0.9105 (tp) cc_final: 0.8757 (tp) REVERT: A 225 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6537 (mp) REVERT: A 271 MET cc_start: 0.7829 (ptt) cc_final: 0.7193 (ptt) REVERT: A 332 ASP cc_start: 0.9236 (m-30) cc_final: 0.8868 (p0) outliers start: 42 outliers final: 30 residues processed: 208 average time/residue: 0.0504 time to fit residues: 15.6273 Evaluate side-chains 207 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 68 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.082365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.072904 restraints weight = 35156.604| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 5.91 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6790 Z= 0.146 Angle : 0.900 15.733 9244 Z= 0.400 Chirality : 0.045 0.249 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.838 58.225 941 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.92 % Allowed : 28.23 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 876 helix: 1.43 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.90 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 431 TYR 0.042 0.002 TYR B 485 PHE 0.027 0.001 PHE B 326 TRP 0.034 0.002 TRP B 392 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6790) covalent geometry : angle 0.89976 ( 9244) hydrogen bonds : bond 0.03839 ( 513) hydrogen bonds : angle 4.23585 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9101 (ttt) cc_final: 0.8832 (mmm) REVERT: B 107 GLU cc_start: 0.7893 (mp0) cc_final: 0.7594 (mp0) REVERT: B 154 LEU cc_start: 0.9339 (mt) cc_final: 0.9104 (mt) REVERT: B 311 ILE cc_start: 0.8833 (tt) cc_final: 0.8586 (pt) REVERT: B 403 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9351 (pt) REVERT: B 456 TRP cc_start: 0.6785 (t-100) cc_final: 0.6511 (t-100) REVERT: B 459 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6137 (mtmt) REVERT: B 472 ASP cc_start: 0.8844 (m-30) cc_final: 0.8571 (m-30) REVERT: A 154 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9188 (mm) REVERT: A 189 LEU cc_start: 0.9171 (tp) cc_final: 0.8837 (tp) REVERT: A 225 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6579 (mp) REVERT: A 271 MET cc_start: 0.7958 (ptt) cc_final: 0.7485 (ptt) REVERT: A 332 ASP cc_start: 0.9204 (m-30) cc_final: 0.8852 (p0) REVERT: A 385 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8519 (mm-30) REVERT: A 431 ARG cc_start: 0.8346 (ptm160) cc_final: 0.7597 (ptm160) outliers start: 35 outliers final: 23 residues processed: 209 average time/residue: 0.0542 time to fit residues: 16.5122 Evaluate side-chains 205 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 494 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.083008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.073537 restraints weight = 35254.707| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.80 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6790 Z= 0.146 Angle : 0.932 13.547 9244 Z= 0.413 Chirality : 0.046 0.266 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.790 58.837 940 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.07 % Allowed : 30.20 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.29), residues: 876 helix: 1.26 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 186 TYR 0.042 0.002 TYR B 485 PHE 0.020 0.001 PHE A 153 TRP 0.021 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6790) covalent geometry : angle 0.93155 ( 9244) hydrogen bonds : bond 0.03879 ( 513) hydrogen bonds : angle 4.28404 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9135 (ttt) cc_final: 0.8868 (mmm) REVERT: B 107 GLU cc_start: 0.7894 (mp0) cc_final: 0.7561 (mp0) REVERT: B 154 LEU cc_start: 0.9274 (mt) cc_final: 0.9047 (mt) REVERT: B 311 ILE cc_start: 0.8845 (tt) cc_final: 0.8603 (pt) REVERT: B 403 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9393 (pt) REVERT: B 456 TRP cc_start: 0.6887 (t-100) cc_final: 0.6568 (t-100) REVERT: B 459 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6184 (mtmt) REVERT: B 472 ASP cc_start: 0.8832 (m-30) cc_final: 0.8552 (m-30) REVERT: A 154 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9200 (mm) REVERT: A 225 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6606 (mp) REVERT: A 271 MET cc_start: 0.8143 (ptt) cc_final: 0.7657 (ptt) REVERT: A 332 ASP cc_start: 0.9263 (m-30) cc_final: 0.8906 (p0) outliers start: 29 outliers final: 23 residues processed: 198 average time/residue: 0.0557 time to fit residues: 16.0292 Evaluate side-chains 201 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 494 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.082888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.073374 restraints weight = 35769.627| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.81 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6790 Z= 0.152 Angle : 1.009 17.254 9244 Z= 0.447 Chirality : 0.049 0.463 1136 Planarity : 0.005 0.045 1122 Dihedral : 5.816 59.726 940 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.21 % Allowed : 31.32 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 876 helix: 1.17 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -2.92 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.046 0.002 TYR B 485 PHE 0.019 0.001 PHE A 153 TRP 0.058 0.002 TRP A 392 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6790) covalent geometry : angle 1.00909 ( 9244) hydrogen bonds : bond 0.03866 ( 513) hydrogen bonds : angle 4.41569 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9102 (ttt) cc_final: 0.8832 (mmm) REVERT: B 107 GLU cc_start: 0.7889 (mp0) cc_final: 0.7619 (mp0) REVERT: B 154 LEU cc_start: 0.9240 (mt) cc_final: 0.9027 (mt) REVERT: B 235 MET cc_start: 0.7617 (mpp) cc_final: 0.7020 (mpp) REVERT: B 311 ILE cc_start: 0.8839 (tt) cc_final: 0.8603 (pt) REVERT: B 456 TRP cc_start: 0.6768 (t-100) cc_final: 0.6478 (t-100) REVERT: B 459 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6136 (mtpt) REVERT: B 472 ASP cc_start: 0.8813 (m-30) cc_final: 0.8504 (m-30) REVERT: A 154 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9156 (mm) REVERT: A 225 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6545 (mp) REVERT: A 271 MET cc_start: 0.7888 (ptt) cc_final: 0.7421 (ptt) REVERT: A 332 ASP cc_start: 0.9125 (m-30) cc_final: 0.8814 (p0) outliers start: 30 outliers final: 24 residues processed: 188 average time/residue: 0.0543 time to fit residues: 14.8986 Evaluate side-chains 198 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 113 ASN B 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.085500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075788 restraints weight = 35707.920| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 5.98 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6790 Z= 0.150 Angle : 1.023 19.173 9244 Z= 0.452 Chirality : 0.047 0.241 1136 Planarity : 0.005 0.045 1122 Dihedral : 5.795 59.575 940 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.51 % Allowed : 31.60 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 876 helix: 1.06 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -2.92 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 475 TYR 0.046 0.002 TYR B 485 PHE 0.018 0.001 PHE A 153 TRP 0.048 0.002 TRP A 392 HIS 0.000 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6790) covalent geometry : angle 1.02301 ( 9244) hydrogen bonds : bond 0.03904 ( 513) hydrogen bonds : angle 4.44831 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9022 (ttt) cc_final: 0.8741 (mmm) REVERT: B 107 GLU cc_start: 0.7921 (mp0) cc_final: 0.7646 (mp0) REVERT: B 271 MET cc_start: 0.8443 (ppp) cc_final: 0.8227 (ppp) REVERT: B 311 ILE cc_start: 0.8804 (tt) cc_final: 0.8576 (pt) REVERT: B 456 TRP cc_start: 0.6685 (t-100) cc_final: 0.6416 (t-100) REVERT: B 459 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6052 (mtpp) REVERT: B 472 ASP cc_start: 0.8755 (m-30) cc_final: 0.8485 (m-30) REVERT: A 154 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9149 (mm) REVERT: A 235 MET cc_start: 0.7826 (ptp) cc_final: 0.7625 (ptp) REVERT: A 271 MET cc_start: 0.7789 (ptt) cc_final: 0.7335 (ptt) REVERT: A 332 ASP cc_start: 0.9118 (m-30) cc_final: 0.8822 (p0) outliers start: 25 outliers final: 21 residues processed: 188 average time/residue: 0.0504 time to fit residues: 14.3387 Evaluate side-chains 193 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.085061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.075435 restraints weight = 36021.301| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 5.98 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6790 Z= 0.157 Angle : 1.047 19.865 9244 Z= 0.461 Chirality : 0.049 0.320 1136 Planarity : 0.005 0.045 1122 Dihedral : 5.809 59.271 940 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.37 % Allowed : 33.15 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.29), residues: 876 helix: 1.05 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.99 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 475 TYR 0.046 0.003 TYR B 485 PHE 0.016 0.002 PHE B 234 TRP 0.041 0.002 TRP A 392 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6790) covalent geometry : angle 1.04720 ( 9244) hydrogen bonds : bond 0.03867 ( 513) hydrogen bonds : angle 4.52256 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.43 seconds wall clock time: 27 minutes 39.15 seconds (1659.15 seconds total)