Starting phenix.real_space_refine on Tue Mar 11 21:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_13161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_13161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_13161.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_13161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1i_13161/03_2025/7p1i_13161.cif" } resolution = 3.15 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= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: B Time building chain proxies: 5.72, per 1000 atoms: 0.86 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: 1.74 Conformation dependent library (CDL) restraints added in 965.6 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: 0.73 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: 2.08 Time building geometry restraints manager: 2.05 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: 0.03 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: 0.790 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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= 0.136 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 (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: 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 TRP 0.011 0.001 TRP A 392 HIS 0.001 0.001 HIS A 477 PHE 0.008 0.001 PHE B 322 TYR 0.004 0.001 TYR A 485 ARG 0.001 0.000 ARG A 431 *********************** 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 : 0.737 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: 0.7521 (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: 0.7283 (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: 0.7953 (tp) REVERT: A 235 MET cc_start: 0.8757 (ttp) cc_final: 0.8486 (ttp) REVERT: A 285 PHE cc_start: 0.8580 (t80) cc_final: 0.8371 (t80) REVERT: A 332 ASP cc_start: 0.9155 (m-30) cc_final: 0.8855 (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: 0.9349 (tt) REVERT: A 385 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8776 (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: 9 residues processed: 311 average time/residue: 0.1541 time to fit residues: 65.7784 Evaluate side-chains 215 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 113 ASN A 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.082579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.073262 restraints weight = 35761.361| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 5.93 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6790 Z= 0.226 Angle : 0.886 15.163 9244 Z= 0.389 Chirality : 0.042 0.226 1136 Planarity : 0.005 0.040 1122 Dihedral : 6.776 65.536 954 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.78 % Allowed : 22.75 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.29), residues: 876 helix: 2.40 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.78 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 377 HIS 0.003 0.001 HIS A 75 PHE 0.034 0.002 PHE B 234 TYR 0.018 0.002 TYR B 260 ARG 0.004 0.000 ARG A 431 *********************** 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 245 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7714 (mp0) cc_final: 0.7487 (mp0) REVERT: B 154 LEU cc_start: 0.9353 (mt) cc_final: 0.9107 (mt) REVERT: B 176 ARG cc_start: 0.8402 (mpp80) cc_final: 0.8168 (mtt-85) REVERT: B 253 LEU cc_start: 0.9443 (mm) cc_final: 0.9154 (pp) REVERT: B 257 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8791 (mt-10) REVERT: B 311 ILE cc_start: 0.8931 (tt) cc_final: 0.8705 (pt) REVERT: B 392 TRP cc_start: 0.9078 (t-100) cc_final: 0.8733 (t-100) REVERT: B 456 TRP cc_start: 0.6960 (t-100) cc_final: 0.6516 (t-100) REVERT: B 459 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6063 (mtmt) REVERT: B 472 ASP cc_start: 0.8808 (m-30) cc_final: 0.8540 (m-30) REVERT: A 107 GLU cc_start: 0.7785 (mp0) cc_final: 0.7321 (mp0) REVERT: A 123 CYS cc_start: 0.9429 (m) cc_final: 0.9201 (p) REVERT: A 131 PHE cc_start: 0.8942 (m-80) cc_final: 0.8715 (m-10) REVERT: A 154 LEU cc_start: 0.9334 (mt) cc_final: 0.9097 (mt) REVERT: A 225 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6770 (tp) REVERT: A 235 MET cc_start: 0.8391 (ttp) cc_final: 0.8023 (ttp) REVERT: A 285 PHE cc_start: 0.8159 (t80) cc_final: 0.7550 (t80) REVERT: A 332 ASP cc_start: 0.9208 (m-30) cc_final: 0.8782 (p0) REVERT: A 372 LEU cc_start: 0.9494 (mm) cc_final: 0.9294 (tt) REVERT: A 407 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7437 (p) outliers start: 34 outliers final: 19 residues processed: 228 average time/residue: 0.1439 time to fit residues: 45.5707 Evaluate side-chains 221 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 178 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 262 VAL Chi-restraints excluded: chain A residue 302 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 0.0060 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 166 GLN ** A 331 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.081413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.072190 restraints weight = 35925.821| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.91 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6790 Z= 0.212 Angle : 0.859 12.941 9244 Z= 0.381 Chirality : 0.043 0.282 1136 Planarity : 0.004 0.043 1122 Dihedral : 6.291 67.238 945 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.90 % Allowed : 23.03 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.63 (0.29), residues: 876 helix: 2.02 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -2.85 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.002 0.000 HIS A 75 PHE 0.039 0.002 PHE B 326 TYR 0.014 0.001 TYR B 260 ARG 0.007 0.000 ARG A 375 *********************** 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 254 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7696 (mp0) cc_final: 0.7469 (mp0) REVERT: B 154 LEU cc_start: 0.9359 (mt) cc_final: 0.9149 (mt) REVERT: B 252 MET cc_start: 0.8268 (tmm) cc_final: 0.8064 (tmm) REVERT: B 311 ILE cc_start: 0.8789 (tt) cc_final: 0.8502 (pt) REVERT: B 365 CYS cc_start: 0.8846 (t) cc_final: 0.8607 (t) REVERT: B 396 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: B 472 ASP cc_start: 0.8756 (m-30) cc_final: 0.8494 (m-30) REVERT: A 107 GLU cc_start: 0.7812 (mp0) cc_final: 0.7339 (mp0) REVERT: A 154 LEU cc_start: 0.9276 (mt) cc_final: 0.9027 (mt) REVERT: A 225 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6786 (tp) REVERT: A 235 MET cc_start: 0.8294 (ttp) cc_final: 0.7982 (ttp) REVERT: A 285 PHE cc_start: 0.8235 (t80) cc_final: 0.7794 (t80) REVERT: A 332 ASP cc_start: 0.9204 (m-30) cc_final: 0.8760 (p0) REVERT: A 466 ILE cc_start: 0.9414 (tp) cc_final: 0.9102 (tp) REVERT: A 511 LEU cc_start: 0.8041 (tp) cc_final: 0.7768 (tp) outliers start: 42 outliers final: 26 residues processed: 231 average time/residue: 0.1372 time to fit residues: 44.5224 Evaluate side-chains 216 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 396 GLN 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 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 178 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 319 LEU 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 444 PHE 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 60 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 396 GLN ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 331 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.078085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.068224 restraints weight = 35722.495| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 6.38 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6790 Z= 0.309 Angle : 0.873 13.585 9244 Z= 0.413 Chirality : 0.046 0.229 1136 Planarity : 0.005 0.042 1122 Dihedral : 5.897 57.394 940 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.46 % Allowed : 24.72 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.29), residues: 876 helix: 1.67 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.77 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 377 HIS 0.004 0.001 HIS A 75 PHE 0.044 0.003 PHE B 326 TYR 0.023 0.002 TYR B 485 ARG 0.006 0.001 ARG B 176 *********************** 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 232 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.8038 (mp0) cc_final: 0.7836 (mp0) REVERT: B 119 MET cc_start: 0.9288 (ptm) cc_final: 0.8997 (ptt) REVERT: B 154 LEU cc_start: 0.9427 (mt) cc_final: 0.9223 (mt) REVERT: B 240 LEU cc_start: 0.8689 (tp) cc_final: 0.8444 (tp) REVERT: B 311 ILE cc_start: 0.8969 (tt) cc_final: 0.8751 (pt) REVERT: B 365 CYS cc_start: 0.9105 (t) cc_final: 0.8776 (t) REVERT: B 392 TRP cc_start: 0.9362 (t-100) cc_final: 0.8965 (t-100) REVERT: B 396 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8999 (pt0) REVERT: B 459 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6232 (mtmt) REVERT: B 472 ASP cc_start: 0.8945 (m-30) cc_final: 0.8695 (m-30) REVERT: A 154 LEU cc_start: 0.9429 (mt) cc_final: 0.9205 (mt) REVERT: A 225 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7018 (tt) REVERT: A 235 MET cc_start: 0.8759 (ttp) cc_final: 0.8407 (ttp) REVERT: A 385 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8679 (mm-30) outliers start: 46 outliers final: 34 residues processed: 212 average time/residue: 0.1276 time to fit residues: 38.7177 Evaluate side-chains 217 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 364 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 396 GLN 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 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 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 319 LEU 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 390 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 494 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.081536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.072049 restraints weight = 34743.831| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 5.89 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4474 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= 0.198 Angle : 0.871 11.678 9244 Z= 0.390 Chirality : 0.045 0.228 1136 Planarity : 0.005 0.067 1122 Dihedral : 5.729 55.557 940 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.78 % Allowed : 26.26 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.29), residues: 876 helix: 1.69 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.80 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 456 HIS 0.001 0.000 HIS A 75 PHE 0.048 0.002 PHE B 326 TYR 0.045 0.002 TYR B 485 ARG 0.004 0.000 ARG A 431 *********************** 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 231 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7779 (mp0) cc_final: 0.7495 (mp0) REVERT: B 119 MET cc_start: 0.9183 (ptm) cc_final: 0.8854 (ptt) REVERT: B 148 MET cc_start: 0.8232 (mtm) cc_final: 0.7780 (mtm) REVERT: B 154 LEU cc_start: 0.9353 (mt) cc_final: 0.9141 (mt) REVERT: B 180 LEU cc_start: 0.9689 (tt) cc_final: 0.9211 (pp) REVERT: B 253 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9039 (mm) REVERT: B 311 ILE cc_start: 0.8798 (tt) cc_final: 0.8576 (pt) REVERT: B 459 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6128 (mtmt) REVERT: B 472 ASP cc_start: 0.8792 (m-30) cc_final: 0.8509 (m-30) REVERT: A 154 LEU cc_start: 0.9455 (mt) cc_final: 0.9201 (mt) REVERT: A 225 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6710 (tp) REVERT: A 332 ASP cc_start: 0.9136 (m-30) cc_final: 0.8811 (p0) outliers start: 34 outliers final: 23 residues processed: 214 average time/residue: 0.1328 time to fit residues: 40.6525 Evaluate side-chains 202 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE 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 398 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 165 ILE Chi-restraints excluded: chain A residue 193 SER 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 319 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.081294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.071801 restraints weight = 35642.746| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.89 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6790 Z= 0.212 Angle : 0.879 12.779 9244 Z= 0.400 Chirality : 0.044 0.221 1136 Planarity : 0.004 0.043 1122 Dihedral : 5.743 55.703 940 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.48 % Allowed : 27.67 % 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 (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: 0.97 (0.29), residues: 876 helix: 1.51 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -2.77 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 PHE 0.047 0.002 PHE B 326 TYR 0.042 0.002 TYR B 485 ARG 0.005 0.000 ARG A 156 *********************** 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 218 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 154 LEU cc_start: 0.9297 (mt) cc_final: 0.9072 (mt) REVERT: B 252 MET cc_start: 0.8744 (ttp) cc_final: 0.8536 (ttt) REVERT: B 311 ILE cc_start: 0.8827 (tt) cc_final: 0.8612 (pt) REVERT: B 459 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6158 (mtmt) REVERT: B 472 ASP cc_start: 0.8767 (m-30) cc_final: 0.8489 (m-30) REVERT: A 96 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9339 (mm) REVERT: A 154 LEU cc_start: 0.9439 (mt) cc_final: 0.9179 (mt) REVERT: A 225 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6544 (mp) REVERT: A 332 ASP cc_start: 0.9179 (m-30) cc_final: 0.8948 (p0) outliers start: 39 outliers final: 28 residues processed: 202 average time/residue: 0.1304 time to fit residues: 37.4750 Evaluate side-chains 206 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 165 ILE 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 396 GLN 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 96 LEU 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 193 SER 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 319 LEU 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 69 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 396 GLN A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.082278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.072667 restraints weight = 34756.532| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.91 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6790 Z= 0.197 Angle : 0.891 14.212 9244 Z= 0.398 Chirality : 0.044 0.236 1136 Planarity : 0.004 0.044 1122 Dihedral : 5.684 54.701 940 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.63 % Allowed : 30.06 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.00 (0.29), residues: 876 helix: 1.52 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 PHE 0.043 0.002 PHE B 326 TYR 0.043 0.002 TYR B 485 ARG 0.003 0.000 ARG B 176 *********************** 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 217 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9133 (ttt) cc_final: 0.8846 (mmm) REVERT: B 107 GLU cc_start: 0.7913 (mp0) cc_final: 0.7566 (mp0) REVERT: B 154 LEU cc_start: 0.9221 (mt) cc_final: 0.8987 (mt) REVERT: B 180 LEU cc_start: 0.9674 (tt) cc_final: 0.9212 (pp) REVERT: B 252 MET cc_start: 0.8771 (ttp) cc_final: 0.8099 (ttp) REVERT: B 311 ILE cc_start: 0.8782 (tt) cc_final: 0.8543 (pt) REVERT: B 459 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6169 (mtpp) REVERT: B 472 ASP cc_start: 0.8811 (m-30) cc_final: 0.8536 (m-30) REVERT: A 96 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9337 (mm) REVERT: A 154 LEU cc_start: 0.9452 (mt) cc_final: 0.9218 (mt) REVERT: A 225 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6524 (mp) REVERT: A 332 ASP cc_start: 0.9180 (m-30) cc_final: 0.8951 (p0) REVERT: A 372 LEU cc_start: 0.9581 (mt) cc_final: 0.9251 (tt) REVERT: A 431 ARG cc_start: 0.8415 (ptm160) cc_final: 0.7549 (ptm160) outliers start: 33 outliers final: 22 residues processed: 203 average time/residue: 0.1347 time to fit residues: 39.4409 Evaluate side-chains 201 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE 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 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 LEU 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 193 SER 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 Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.080729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.071035 restraints weight = 35397.676| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 6.02 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6790 Z= 0.272 Angle : 0.939 14.539 9244 Z= 0.432 Chirality : 0.046 0.288 1136 Planarity : 0.005 0.043 1122 Dihedral : 5.906 57.921 940 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.21 % Allowed : 30.90 % 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 (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: 0.79 (0.29), residues: 876 helix: 1.33 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.60 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 392 HIS 0.003 0.001 HIS A 75 PHE 0.029 0.002 PHE B 326 TYR 0.042 0.002 TYR B 485 ARG 0.003 0.000 ARG A 186 *********************** 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 205 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.8167 (mp0) cc_final: 0.7942 (mp0) REVERT: B 240 LEU cc_start: 0.8610 (tp) cc_final: 0.8393 (tp) REVERT: B 252 MET cc_start: 0.8873 (ttp) cc_final: 0.8583 (ttp) REVERT: B 311 ILE cc_start: 0.8823 (tt) cc_final: 0.8600 (pt) REVERT: B 444 PHE cc_start: 0.7404 (m-80) cc_final: 0.7165 (m-10) REVERT: B 459 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6258 (mtmt) REVERT: B 472 ASP cc_start: 0.8951 (m-30) cc_final: 0.8685 (m-30) REVERT: A 96 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9438 (mm) REVERT: A 189 LEU cc_start: 0.9252 (tp) cc_final: 0.8994 (tp) REVERT: A 225 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 332 ASP cc_start: 0.9371 (m-30) cc_final: 0.9079 (p0) REVERT: A 431 ARG cc_start: 0.8789 (ptm160) cc_final: 0.7845 (ptm160) outliers start: 30 outliers final: 24 residues processed: 193 average time/residue: 0.1358 time to fit residues: 37.1998 Evaluate side-chains 199 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE 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 396 GLN 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 96 LEU 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 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 481 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN A 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.082030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.072467 restraints weight = 34981.348| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 5.97 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5144 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= 0.214 Angle : 0.977 14.801 9244 Z= 0.431 Chirality : 0.047 0.498 1136 Planarity : 0.004 0.043 1122 Dihedral : 5.900 56.980 940 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.65 % Allowed : 31.60 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.78 (0.29), residues: 876 helix: 1.34 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -2.68 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 PHE 0.021 0.002 PHE B 115 TYR 0.044 0.002 TYR B 485 ARG 0.003 0.000 ARG B 176 *********************** 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 206 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9206 (ttt) cc_final: 0.8920 (mmm) REVERT: B 107 GLU cc_start: 0.8115 (mp0) cc_final: 0.7880 (mp0) REVERT: B 148 MET cc_start: 0.8091 (mtm) cc_final: 0.7750 (mtm) REVERT: B 252 MET cc_start: 0.8823 (ttp) cc_final: 0.8475 (ttp) REVERT: B 311 ILE cc_start: 0.8771 (tt) cc_final: 0.8548 (pt) REVERT: B 438 MET cc_start: 0.7775 (tmm) cc_final: 0.7369 (ttt) REVERT: B 456 TRP cc_start: 0.6695 (t-100) cc_final: 0.6392 (t-100) REVERT: B 459 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6334 (mtpp) REVERT: B 472 ASP cc_start: 0.8885 (m-30) cc_final: 0.8568 (m-30) REVERT: A 189 LEU cc_start: 0.9230 (tp) cc_final: 0.9010 (tp) REVERT: A 225 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6820 (mp) REVERT: A 271 MET cc_start: 0.8212 (ptt) cc_final: 0.7779 (ptt) REVERT: A 332 ASP cc_start: 0.9276 (m-30) cc_final: 0.9012 (p0) outliers start: 26 outliers final: 19 residues processed: 197 average time/residue: 0.1391 time to fit residues: 38.7556 Evaluate side-chains 193 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 396 GLN 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 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 382 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.083156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.073682 restraints weight = 36119.802| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 5.83 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5309 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= 0.217 Angle : 0.981 13.874 9244 Z= 0.435 Chirality : 0.047 0.289 1136 Planarity : 0.004 0.043 1122 Dihedral : 5.842 56.611 940 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.95 % Allowed : 32.30 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.71 (0.29), residues: 876 helix: 1.31 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.71 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 392 HIS 0.001 0.000 HIS A 75 PHE 0.022 0.002 PHE B 451 TYR 0.046 0.002 TYR B 485 ARG 0.011 0.001 ARG B 475 ********************** 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: 21 poor density : 177 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9004 (ttt) cc_final: 0.8765 (mmm) REVERT: B 107 GLU cc_start: 0.7999 (mp0) cc_final: 0.7746 (mp0) REVERT: B 154 LEU cc_start: 0.9220 (mm) cc_final: 0.8998 (mm) REVERT: B 252 MET cc_start: 0.8472 (ttp) cc_final: 0.8111 (ttp) REVERT: B 311 ILE cc_start: 0.8757 (tt) cc_final: 0.8538 (pt) REVERT: B 438 MET cc_start: 0.7603 (tmm) cc_final: 0.7152 (ttt) REVERT: B 459 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6244 (mtpp) REVERT: B 472 ASP cc_start: 0.8655 (m-30) cc_final: 0.8399 (m-30) REVERT: A 225 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6513 (mp) REVERT: A 271 MET cc_start: 0.7814 (ptt) cc_final: 0.7434 (ptt) outliers start: 21 outliers final: 18 residues processed: 191 average time/residue: 0.1311 time to fit residues: 35.9643 Evaluate side-chains 191 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 396 GLN 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 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 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 36 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 0.0570 chunk 31 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.081441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.072220 restraints weight = 36132.076| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 5.61 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6790 Z= 0.261 Angle : 0.981 13.521 9244 Z= 0.442 Chirality : 0.048 0.269 1136 Planarity : 0.004 0.043 1122 Dihedral : 5.963 59.061 940 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.09 % Allowed : 33.43 % 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 (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: 0.66 (0.29), residues: 876 helix: 1.27 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.69 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 392 HIS 0.002 0.001 HIS A 75 PHE 0.019 0.002 PHE B 115 TYR 0.046 0.002 TYR B 485 ARG 0.004 0.000 ARG B 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.07 seconds wall clock time: 54 minutes 29.53 seconds (3269.53 seconds total)