Starting phenix.real_space_refine on Tue Feb 13 15:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_13161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_13161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_13161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_13161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/02_2024/7p1i_13161.pdb" } 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 Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 2 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 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 Time building chain proxies: 3.99, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.55 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: 1.71 Time building geometry restraints manager: 2.92 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: 100.38 - 107.10: 212 107.10 - 113.82: 3972 113.82 - 120.55: 2703 120.55 - 127.27: 2275 127.27 - 133.99: 82 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 2.520 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.265 2.520 nonbonded pdb=" OG SER A 353 " pdb=" O PHE A 358 " model vdw 2.345 2.440 nonbonded pdb=" OG SER B 353 " pdb=" O PHE B 358 " model vdw 2.345 2.440 nonbonded pdb=" NH1 ARG B 431 " pdb=" O TRP B 456 " model vdw 2.368 2.520 ... (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 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.170 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 0.771 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: 0.1621 time to fit residues: 68.1517 Evaluate side-chains 215 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 overall best weight: 3.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN B 481 GLN A 89 ASN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3276 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= 0.293 Angle : 0.866 12.985 9244 Z= 0.396 Chirality : 0.042 0.196 1136 Planarity : 0.005 0.041 1122 Dihedral : 6.880 68.164 954 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 7.30 % Allowed : 22.89 % Favored : 69.80 % 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: 2.09 (0.30), residues: 876 helix: 2.38 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.89 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 230 HIS 0.004 0.001 HIS A 75 PHE 0.029 0.002 PHE B 234 TYR 0.014 0.002 TYR B 260 ARG 0.005 0.001 ARG B 156 *********************** 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 250 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 0.753 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: 0.7630 (mp0) cc_final: 0.7388 (mp0) REVERT: B 148 MET cc_start: 0.8423 (mtp) cc_final: 0.8039 (mpp) REVERT: B 154 LEU cc_start: 0.9218 (mt) cc_final: 0.8943 (mt) REVERT: B 253 LEU cc_start: 0.9382 (mm) cc_final: 0.8995 (mt) REVERT: B 260 TYR cc_start: 0.6747 (m-10) cc_final: 0.6535 (m-10) REVERT: B 311 ILE cc_start: 0.8995 (tt) cc_final: 0.8700 (pt) REVERT: B 454 PHE cc_start: 0.8224 (m-80) cc_final: 0.7991 (m-80) REVERT: B 456 TRP cc_start: 0.7263 (t-100) cc_final: 0.6754 (t-100) REVERT: B 459 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.5643 (mtmt) REVERT: B 472 ASP cc_start: 0.8734 (m-30) cc_final: 0.8515 (m-30) REVERT: A 107 GLU cc_start: 0.7634 (mp0) cc_final: 0.7264 (mp0) REVERT: A 123 CYS cc_start: 0.9576 (m) cc_final: 0.9214 (p) REVERT: A 154 LEU cc_start: 0.9367 (mt) cc_final: 0.9136 (mt) REVERT: A 225 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 235 MET cc_start: 0.8854 (ttp) cc_final: 0.8454 (ttp) REVERT: A 285 PHE cc_start: 0.8734 (t80) cc_final: 0.8196 (t80) REVERT: A 332 ASP cc_start: 0.9328 (m-30) cc_final: 0.8881 (p0) REVERT: A 385 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8807 (mm-30) outliers start: 52 outliers final: 35 residues processed: 226 average time/residue: 0.1405 time to fit residues: 44.3638 Evaluate side-chains 219 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 203 CYS 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 383 ASP 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 B residue 481 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 LEU 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 268 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU 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 396 GLN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 481 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 89 ASN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6790 Z= 0.212 Angle : 0.813 11.517 9244 Z= 0.368 Chirality : 0.042 0.216 1136 Planarity : 0.004 0.041 1122 Dihedral : 6.107 69.107 944 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.62 % Allowed : 23.88 % Favored : 70.51 % 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: 1.74 (0.29), residues: 876 helix: 2.12 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.004 0.001 HIS A 75 PHE 0.039 0.002 PHE B 326 TYR 0.009 0.001 TYR B 260 ARG 0.005 0.001 ARG B 176 *********************** 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 237 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7539 (mp0) cc_final: 0.7325 (mp0) REVERT: B 154 LEU cc_start: 0.9217 (mt) cc_final: 0.8970 (mt) REVERT: B 252 MET cc_start: 0.8550 (tmm) cc_final: 0.7345 (tmm) REVERT: B 396 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: B 454 PHE cc_start: 0.8253 (m-80) cc_final: 0.8043 (m-80) REVERT: B 456 TRP cc_start: 0.7170 (t-100) cc_final: 0.6896 (t-100) REVERT: B 459 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5765 (mtmt) REVERT: B 472 ASP cc_start: 0.8709 (m-30) cc_final: 0.8465 (m-30) REVERT: A 107 GLU cc_start: 0.7694 (mp0) cc_final: 0.7296 (mp0) REVERT: A 123 CYS cc_start: 0.9597 (m) cc_final: 0.9298 (p) REVERT: A 154 LEU cc_start: 0.9342 (mt) cc_final: 0.9110 (mt) REVERT: A 225 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 235 MET cc_start: 0.8821 (ttp) cc_final: 0.8518 (ttp) REVERT: A 332 ASP cc_start: 0.9290 (m-30) cc_final: 0.8824 (p0) REVERT: A 451 PHE cc_start: 0.9068 (t80) cc_final: 0.8539 (t80) REVERT: A 511 LEU cc_start: 0.8364 (tp) cc_final: 0.8063 (tp) outliers start: 40 outliers final: 29 residues processed: 216 average time/residue: 0.1378 time to fit residues: 42.0655 Evaluate side-chains 211 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE 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 331 GLN Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 ASP 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 113 ASN 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 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 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 444 PHE Chi-restraints excluded: chain A residue 494 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 79 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6790 Z= 0.194 Angle : 0.824 11.363 9244 Z= 0.374 Chirality : 0.042 0.204 1136 Planarity : 0.004 0.042 1122 Dihedral : 5.527 51.951 941 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.20 % Allowed : 24.86 % Favored : 69.94 % 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: 1.56 (0.29), residues: 876 helix: 1.99 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.98 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 377 HIS 0.002 0.000 HIS A 75 PHE 0.052 0.002 PHE B 326 TYR 0.013 0.001 TYR B 260 ARG 0.009 0.001 ARG B 338 *********************** 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 fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7540 (mp0) cc_final: 0.7285 (mp0) REVERT: B 154 LEU cc_start: 0.9267 (mt) cc_final: 0.9007 (mt) REVERT: B 252 MET cc_start: 0.8435 (tmm) cc_final: 0.8235 (ttp) REVERT: B 392 TRP cc_start: 0.8951 (t-100) cc_final: 0.8636 (t-100) REVERT: B 396 GLN cc_start: 0.9262 (tt0) cc_final: 0.9027 (pt0) REVERT: B 454 PHE cc_start: 0.8278 (m-80) cc_final: 0.8066 (m-80) REVERT: B 456 TRP cc_start: 0.7125 (t-100) cc_final: 0.6739 (t-100) REVERT: B 459 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.5867 (mtmt) REVERT: B 472 ASP cc_start: 0.8702 (m-30) cc_final: 0.8444 (m-30) REVERT: A 107 GLU cc_start: 0.7776 (mp0) cc_final: 0.7324 (mp0) REVERT: A 123 CYS cc_start: 0.9573 (m) cc_final: 0.9287 (p) REVERT: A 153 PHE cc_start: 0.8872 (t80) cc_final: 0.8485 (t80) REVERT: A 154 LEU cc_start: 0.9464 (mt) cc_final: 0.9116 (mt) REVERT: A 189 LEU cc_start: 0.9178 (tp) cc_final: 0.8971 (tp) REVERT: A 225 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 332 ASP cc_start: 0.9283 (m-30) cc_final: 0.8836 (p0) REVERT: A 397 PRO cc_start: 0.9201 (Cg_exo) cc_final: 0.8974 (Cg_endo) REVERT: A 451 PHE cc_start: 0.9053 (t80) cc_final: 0.8358 (t80) REVERT: A 511 LEU cc_start: 0.8363 (tp) cc_final: 0.7965 (tp) outliers start: 37 outliers final: 26 residues processed: 213 average time/residue: 0.1289 time to fit residues: 39.4812 Evaluate side-chains 213 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 330 ASP 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 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 302 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LEU 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 444 PHE Chi-restraints excluded: chain A residue 494 PHE 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 48 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4330 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= 0.200 Angle : 0.845 12.673 9244 Z= 0.385 Chirality : 0.043 0.275 1136 Planarity : 0.004 0.041 1122 Dihedral : 5.536 52.541 940 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.62 % Allowed : 25.70 % Favored : 68.68 % 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: 1.38 (0.29), residues: 876 helix: 1.85 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -3.01 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 PHE 0.052 0.002 PHE B 326 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG B 176 *********************** 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 228 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7574 (mp0) cc_final: 0.7244 (mp0) REVERT: B 154 LEU cc_start: 0.9169 (mt) cc_final: 0.8912 (mt) REVERT: B 396 GLN cc_start: 0.9289 (tt0) cc_final: 0.8863 (tm-30) REVERT: B 454 PHE cc_start: 0.8286 (m-80) cc_final: 0.8047 (m-80) REVERT: B 456 TRP cc_start: 0.7081 (t-100) cc_final: 0.6631 (t-100) REVERT: B 459 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5873 (mtmt) REVERT: B 472 ASP cc_start: 0.8696 (m-30) cc_final: 0.8432 (m-30) REVERT: A 107 GLU cc_start: 0.7843 (mp0) cc_final: 0.7323 (mp0) REVERT: A 123 CYS cc_start: 0.9568 (m) cc_final: 0.9293 (p) REVERT: A 154 LEU cc_start: 0.9446 (mt) cc_final: 0.9160 (mt) REVERT: A 225 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8143 (tp) REVERT: A 330 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 332 ASP cc_start: 0.9331 (m-30) cc_final: 0.8924 (p0) REVERT: A 431 ARG cc_start: 0.8596 (ptm160) cc_final: 0.7653 (ptm160) REVERT: A 451 PHE cc_start: 0.9055 (t80) cc_final: 0.8336 (t80) REVERT: A 511 LEU cc_start: 0.8460 (tp) cc_final: 0.8064 (tp) outliers start: 40 outliers final: 30 residues processed: 206 average time/residue: 0.1291 time to fit residues: 37.9199 Evaluate side-chains 210 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 330 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 ASP 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 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 269 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 330 ASP 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 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 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6790 Z= 0.188 Angle : 0.854 13.662 9244 Z= 0.387 Chirality : 0.042 0.207 1136 Planarity : 0.004 0.041 1122 Dihedral : 5.485 51.178 940 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.62 % Allowed : 27.67 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.29), residues: 876 helix: 1.78 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.96 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 392 HIS 0.001 0.000 HIS A 75 PHE 0.051 0.002 PHE B 326 TYR 0.012 0.001 TYR A 260 ARG 0.004 0.000 ARG B 176 *********************** 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 223 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7541 (mp0) cc_final: 0.7249 (mp0) REVERT: B 154 LEU cc_start: 0.9161 (mt) cc_final: 0.8904 (mt) REVERT: B 392 TRP cc_start: 0.8982 (t-100) cc_final: 0.8483 (t-100) REVERT: B 396 GLN cc_start: 0.9261 (tt0) cc_final: 0.8588 (tm-30) REVERT: B 454 PHE cc_start: 0.8254 (m-80) cc_final: 0.8025 (m-80) REVERT: B 456 TRP cc_start: 0.7054 (t-100) cc_final: 0.6581 (t-100) REVERT: B 459 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.5850 (mtmt) REVERT: A 107 GLU cc_start: 0.7834 (mp0) cc_final: 0.7231 (mp0) REVERT: A 123 CYS cc_start: 0.9541 (m) cc_final: 0.9265 (p) REVERT: A 154 LEU cc_start: 0.9457 (mt) cc_final: 0.9242 (mt) REVERT: A 225 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8103 (tp) REVERT: A 332 ASP cc_start: 0.9332 (m-30) cc_final: 0.8982 (p0) REVERT: A 431 ARG cc_start: 0.8517 (ptm160) cc_final: 0.7595 (ptm160) REVERT: A 451 PHE cc_start: 0.9054 (t80) cc_final: 0.8368 (t80) REVERT: A 511 LEU cc_start: 0.8498 (tp) cc_final: 0.8148 (tp) outliers start: 40 outliers final: 27 residues processed: 204 average time/residue: 0.1409 time to fit residues: 40.5591 Evaluate side-chains 207 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 199 LEU 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 269 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU 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 396 GLN Chi-restraints excluded: chain A residue 444 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 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4752 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= 0.205 Angle : 0.899 14.616 9244 Z= 0.406 Chirality : 0.044 0.282 1136 Planarity : 0.004 0.039 1122 Dihedral : 5.498 51.926 940 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.06 % Allowed : 28.79 % Favored : 66.15 % 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: 1.10 (0.28), residues: 876 helix: 1.63 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.99 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 392 HIS 0.001 0.000 HIS A 75 PHE 0.048 0.002 PHE B 326 TYR 0.013 0.001 TYR B 260 ARG 0.009 0.001 ARG A 156 *********************** 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 218 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9127 (ttt) cc_final: 0.8816 (mmm) REVERT: B 107 GLU cc_start: 0.7613 (mp0) cc_final: 0.7292 (mp0) REVERT: B 154 LEU cc_start: 0.9010 (mt) cc_final: 0.8740 (mt) REVERT: B 396 GLN cc_start: 0.9287 (tt0) cc_final: 0.8878 (pt0) REVERT: B 454 PHE cc_start: 0.8237 (m-80) cc_final: 0.8020 (m-80) REVERT: B 456 TRP cc_start: 0.7058 (t-100) cc_final: 0.6576 (t-100) REVERT: B 459 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.5838 (mtmt) REVERT: A 107 GLU cc_start: 0.7841 (mp0) cc_final: 0.7267 (mp0) REVERT: A 123 CYS cc_start: 0.9522 (m) cc_final: 0.9255 (p) REVERT: A 154 LEU cc_start: 0.9388 (mt) cc_final: 0.9172 (mt) REVERT: A 332 ASP cc_start: 0.9312 (m-30) cc_final: 0.8929 (p0) REVERT: A 385 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8841 (mm-30) REVERT: A 451 PHE cc_start: 0.9052 (t80) cc_final: 0.8366 (t80) REVERT: A 511 LEU cc_start: 0.8485 (tp) cc_final: 0.8131 (tp) outliers start: 36 outliers final: 27 residues processed: 201 average time/residue: 0.1345 time to fit residues: 38.7904 Evaluate side-chains 202 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 330 ASP Chi-restraints excluded: chain B residue 383 ASP 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 86 VAL 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 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 317 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 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 50 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.0170 chunk 53 optimal weight: 0.0670 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6790 Z= 0.217 Angle : 0.920 14.662 9244 Z= 0.416 Chirality : 0.045 0.305 1136 Planarity : 0.004 0.041 1122 Dihedral : 5.205 51.156 938 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.63 % Allowed : 30.90 % 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 (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: 0.98 (0.28), residues: 876 helix: 1.56 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -3.05 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 392 HIS 0.001 0.000 HIS A 75 PHE 0.047 0.002 PHE B 326 TYR 0.013 0.001 TYR A 260 ARG 0.008 0.000 ARG A 156 *********************** 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 fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9137 (ttt) cc_final: 0.8848 (mmm) REVERT: B 107 GLU cc_start: 0.7610 (mp0) cc_final: 0.7288 (mp0) REVERT: B 154 LEU cc_start: 0.8988 (mt) cc_final: 0.8722 (mt) REVERT: B 252 MET cc_start: 0.8694 (tmm) cc_final: 0.7832 (tmm) REVERT: B 308 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 365 CYS cc_start: 0.9138 (p) cc_final: 0.8307 (t) REVERT: B 396 GLN cc_start: 0.9298 (tt0) cc_final: 0.8991 (pt0) REVERT: B 454 PHE cc_start: 0.8246 (m-80) cc_final: 0.8039 (m-80) REVERT: B 456 TRP cc_start: 0.7057 (t-100) cc_final: 0.6574 (t-100) REVERT: B 459 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5703 (mtmt) REVERT: A 107 GLU cc_start: 0.7857 (mp0) cc_final: 0.7283 (mp0) REVERT: A 123 CYS cc_start: 0.9526 (m) cc_final: 0.9272 (p) REVERT: A 332 ASP cc_start: 0.9305 (m-30) cc_final: 0.8941 (p0) REVERT: A 385 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8856 (mm-30) REVERT: A 396 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: A 451 PHE cc_start: 0.9058 (t80) cc_final: 0.8401 (t80) REVERT: A 511 LEU cc_start: 0.8508 (tp) cc_final: 0.8138 (tp) outliers start: 33 outliers final: 22 residues processed: 193 average time/residue: 0.1328 time to fit residues: 36.7452 Evaluate side-chains 194 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 383 ASP 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 86 VAL 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 226 MET Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU 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 396 GLN Chi-restraints excluded: chain A residue 444 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5097 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= 0.226 Angle : 0.970 15.829 9244 Z= 0.438 Chirality : 0.048 0.400 1136 Planarity : 0.004 0.040 1122 Dihedral : 5.181 51.164 938 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.93 % Allowed : 31.60 % 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 (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: 0.88 (0.29), residues: 876 helix: 1.50 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -3.10 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 392 HIS 0.001 0.000 HIS A 75 PHE 0.042 0.002 PHE B 326 TYR 0.016 0.001 TYR A 260 ARG 0.006 0.000 ARG A 156 *********************** 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 fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 92 MET cc_start: 0.9139 (ttt) cc_final: 0.8848 (mmm) REVERT: B 107 GLU cc_start: 0.7636 (mp0) cc_final: 0.7305 (mp0) REVERT: B 154 LEU cc_start: 0.8982 (mt) cc_final: 0.8711 (mt) REVERT: B 252 MET cc_start: 0.8629 (tmm) cc_final: 0.8271 (tmm) REVERT: B 396 GLN cc_start: 0.9298 (tt0) cc_final: 0.8985 (pt0) REVERT: B 454 PHE cc_start: 0.8246 (m-80) cc_final: 0.8046 (m-80) REVERT: B 456 TRP cc_start: 0.7020 (t-100) cc_final: 0.6530 (t-100) REVERT: B 459 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.5801 (mtmt) REVERT: A 107 GLU cc_start: 0.7843 (mp0) cc_final: 0.7317 (mp0) REVERT: A 123 CYS cc_start: 0.9523 (m) cc_final: 0.9263 (p) REVERT: A 332 ASP cc_start: 0.9317 (m-30) cc_final: 0.8977 (p0) REVERT: A 385 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8838 (mm-30) REVERT: A 396 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7532 (mm110) REVERT: A 451 PHE cc_start: 0.9065 (t80) cc_final: 0.8427 (t80) REVERT: A 511 LEU cc_start: 0.8514 (tp) cc_final: 0.8153 (tp) outliers start: 28 outliers final: 23 residues processed: 191 average time/residue: 0.1359 time to fit residues: 36.8051 Evaluate side-chains 195 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 383 ASP 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 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 268 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU 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 396 GLN Chi-restraints excluded: chain A residue 444 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 7 optimal weight: 0.3980 chunk 53 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6790 Z= 0.228 Angle : 1.040 16.697 9244 Z= 0.467 Chirality : 0.050 0.333 1136 Planarity : 0.004 0.039 1122 Dihedral : 5.179 50.141 938 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.51 % Allowed : 32.72 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -3.21 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 456 HIS 0.000 0.000 HIS A 75 PHE 0.038 0.002 PHE B 326 TYR 0.018 0.001 TYR A 260 ARG 0.005 0.000 ARG A 156 ********************** 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 199 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9127 (ttt) cc_final: 0.8849 (mmm) REVERT: B 107 GLU cc_start: 0.7592 (mp0) cc_final: 0.7272 (mp0) REVERT: B 154 LEU cc_start: 0.8940 (mt) cc_final: 0.8667 (mt) REVERT: B 396 GLN cc_start: 0.9324 (tt0) cc_final: 0.8977 (pt0) REVERT: B 456 TRP cc_start: 0.7031 (t-100) cc_final: 0.6567 (t-100) REVERT: B 459 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5768 (mtmt) REVERT: A 107 GLU cc_start: 0.7848 (mp0) cc_final: 0.7315 (mp0) REVERT: A 123 CYS cc_start: 0.9500 (m) cc_final: 0.9257 (p) REVERT: A 332 ASP cc_start: 0.9310 (m-30) cc_final: 0.8996 (p0) REVERT: A 372 LEU cc_start: 0.9628 (mt) cc_final: 0.9250 (tt) REVERT: A 385 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8864 (mm-30) REVERT: A 451 PHE cc_start: 0.9064 (t80) cc_final: 0.8441 (t80) REVERT: A 511 LEU cc_start: 0.8507 (tp) cc_final: 0.8159 (tp) outliers start: 25 outliers final: 21 residues processed: 190 average time/residue: 0.1295 time to fit residues: 35.6229 Evaluate side-chains 189 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 383 ASP 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 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 268 THR Chi-restraints excluded: chain A residue 269 LEU 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 396 GLN Chi-restraints excluded: chain A residue 444 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.084599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.074896 restraints weight = 35643.037| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 6.02 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6790 Z= 0.227 Angle : 1.051 18.449 9244 Z= 0.470 Chirality : 0.051 0.509 1136 Planarity : 0.004 0.040 1122 Dihedral : 4.930 46.286 936 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.37 % Allowed : 33.01 % Favored : 63.62 % 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: 0.45 (0.28), residues: 876 helix: 1.21 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -3.22 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 392 HIS 0.001 0.000 HIS A 75 PHE 0.022 0.001 PHE B 115 TYR 0.016 0.001 TYR A 260 ARG 0.005 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.91 seconds wall clock time: 30 minutes 54.68 seconds (1854.68 seconds total)