Starting phenix.real_space_refine on Tue Feb 11 21:43:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1i_13161/02_2025/7p1i_13161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1i_13161/02_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_13161/02_2025/7p1i_13161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1i_13161/02_2025/7p1i_13161.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1i_13161/02_2025/7p1i_13161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1i_13161/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.54, per 1000 atoms: 0.83 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: 1.62 Conformation dependent library (CDL) restraints added in 1.1 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: 0.63 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: 1.85 Time building geometry restraints manager: 1.90 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: 0.580 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- 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 : 0.882 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: 0.1702 time to fit residues: 71.5453 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 : 0.752 ------------------------------------------------------------------------------- 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 = 0.073261 restraints weight = 35761.360| |-----------------------------------------------------------------------------| 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 : 0.798 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: 0.8401 (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: 0.9079 (t-100) cc_final: 0.8733 (t-100) REVERT: B 456 TRP cc_start: 0.6960 (t-100) cc_final: 0.6515 (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: 0.7322 (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: 0.8392 (ttp) cc_final: 0.8024 (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 407 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7437 (p) outliers start: 34 outliers final: 19 residues processed: 228 average time/residue: 0.1515 time to fit residues: 47.7693 Evaluate side-chains 220 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.081375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.072137 restraints weight = 35902.636| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 5.93 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3761 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= 0.211 Angle : 0.855 12.845 9244 Z= 0.379 Chirality : 0.043 0.274 1136 Planarity : 0.004 0.042 1122 Dihedral : 6.299 67.262 945 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.04 % Allowed : 22.61 % Favored : 71.35 % 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: 1.59 (0.29), residues: 876 helix: 1.99 (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 0.038 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 255 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7714 (mp0) cc_final: 0.7488 (mp0) REVERT: B 154 LEU cc_start: 0.9364 (mt) cc_final: 0.9157 (mt) REVERT: B 176 ARG cc_start: 0.8457 (mpp80) cc_final: 0.8254 (mtt-85) REVERT: B 311 ILE cc_start: 0.8789 (tt) cc_final: 0.8499 (pt) REVERT: B 365 CYS cc_start: 0.8878 (t) cc_final: 0.8636 (t) REVERT: B 459 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6148 (mtmt) REVERT: B 472 ASP cc_start: 0.8778 (m-30) cc_final: 0.8515 (m-30) REVERT: A 107 GLU cc_start: 0.7809 (mp0) cc_final: 0.7347 (mp0) REVERT: A 154 LEU cc_start: 0.9308 (mt) cc_final: 0.9061 (mt) REVERT: A 225 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6852 (tp) REVERT: A 235 MET cc_start: 0.8342 (ttp) cc_final: 0.8027 (ttp) REVERT: A 285 PHE cc_start: 0.8251 (t80) cc_final: 0.7820 (t80) REVERT: A 332 ASP cc_start: 0.9192 (m-30) cc_final: 0.8751 (p0) REVERT: A 466 ILE cc_start: 0.9426 (tp) cc_final: 0.9115 (tp) REVERT: A 511 LEU cc_start: 0.8058 (tp) cc_final: 0.7788 (tp) outliers start: 43 outliers final: 24 residues processed: 232 average time/residue: 0.1446 time to fit residues: 47.1046 Evaluate side-chains 215 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.114927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.107296 restraints weight = 40300.135| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.71 r_work: 0.3690 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4468 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= 0.335 Angle : 0.880 15.239 9244 Z= 0.420 Chirality : 0.046 0.216 1136 Planarity : 0.005 0.043 1122 Dihedral : 6.077 59.275 940 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 7.16 % Allowed : 24.16 % 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: 1.04 (0.29), residues: 876 helix: 1.54 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.68 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 392 HIS 0.005 0.001 HIS A 75 PHE 0.039 0.003 PHE B 326 TYR 0.021 0.002 TYR B 485 ARG 0.008 0.001 ARG A 156 *********************** 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 241 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7947 (mp0) cc_final: 0.7730 (mp0) REVERT: B 119 MET cc_start: 0.9387 (ptm) cc_final: 0.9121 (ptt) REVERT: B 240 LEU cc_start: 0.8753 (tp) cc_final: 0.8510 (tp) REVERT: B 365 CYS cc_start: 0.9230 (t) cc_final: 0.8946 (t) REVERT: B 459 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6114 (mtmt) REVERT: B 472 ASP cc_start: 0.8896 (m-30) cc_final: 0.8646 (m-30) REVERT: A 154 LEU cc_start: 0.9423 (mt) cc_final: 0.9215 (mt) REVERT: A 225 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7345 (tp) REVERT: A 235 MET cc_start: 0.8916 (ttp) cc_final: 0.8635 (ttp) REVERT: A 385 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8833 (mm-30) REVERT: A 454 PHE cc_start: 0.8269 (m-80) cc_final: 0.7860 (m-80) outliers start: 51 outliers final: 38 residues processed: 217 average time/residue: 0.1412 time to fit residues: 43.2283 Evaluate side-chains 217 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 364 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 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 244 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 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: 7.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.079602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.070418 restraints weight = 35656.025| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 5.69 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4627 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= 0.224 Angle : 0.873 14.062 9244 Z= 0.392 Chirality : 0.045 0.248 1136 Planarity : 0.004 0.044 1122 Dihedral : 5.956 59.275 940 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.48 % Allowed : 27.11 % Favored : 67.42 % 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 (0.29), residues: 876 helix: 1.59 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 392 HIS 0.002 0.001 HIS A 75 PHE 0.046 0.002 PHE B 326 TYR 0.046 0.002 TYR B 485 ARG 0.003 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 225 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7908 (mp0) cc_final: 0.7642 (mp0) REVERT: B 119 MET cc_start: 0.9182 (ptm) cc_final: 0.8861 (ptt) REVERT: B 365 CYS cc_start: 0.8953 (t) cc_final: 0.8730 (t) REVERT: B 459 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6191 (mtpp) REVERT: B 472 ASP cc_start: 0.8853 (m-30) cc_final: 0.8595 (m-30) REVERT: A 154 LEU cc_start: 0.9479 (mt) cc_final: 0.9235 (mt) REVERT: A 171 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.7667 (m-90) REVERT: A 211 CYS cc_start: 0.8491 (m) cc_final: 0.8288 (t) REVERT: A 225 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6648 (mp) REVERT: A 331 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: A 332 ASP cc_start: 0.9248 (m-30) cc_final: 0.8935 (p0) outliers start: 39 outliers final: 28 residues processed: 209 average time/residue: 0.1442 time to fit residues: 42.5593 Evaluate side-chains 204 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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 171 TRP 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 234 PHE 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 331 GLN 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: 6.9990 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.080654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.071421 restraints weight = 35839.526| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 5.77 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4848 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= 0.215 Angle : 0.879 12.883 9244 Z= 0.396 Chirality : 0.044 0.218 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.941 58.972 940 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.90 % Allowed : 28.79 % 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: 0.96 (0.29), residues: 876 helix: 1.50 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 392 HIS 0.006 0.001 HIS A 75 PHE 0.045 0.002 PHE B 326 TYR 0.043 0.002 TYR B 485 ARG 0.004 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 223 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.7905 (mp0) cc_final: 0.7624 (mp0) REVERT: B 252 MET cc_start: 0.8634 (ttt) cc_final: 0.7600 (ttt) REVERT: B 365 CYS cc_start: 0.8833 (t) cc_final: 0.8607 (t) REVERT: B 396 GLN cc_start: 0.8537 (pt0) cc_final: 0.8327 (pt0) REVERT: B 456 TRP cc_start: 0.6638 (t-100) cc_final: 0.6368 (t-100) REVERT: B 459 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6244 (mtmt) REVERT: B 472 ASP cc_start: 0.8774 (m-30) cc_final: 0.8511 (m-30) REVERT: A 154 LEU cc_start: 0.9464 (mt) cc_final: 0.9200 (mt) REVERT: A 171 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.7592 (m-90) REVERT: A 189 LEU cc_start: 0.9007 (tp) cc_final: 0.8778 (tp) REVERT: A 225 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6546 (mp) REVERT: A 331 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: A 332 ASP cc_start: 0.9155 (m-30) cc_final: 0.8920 (p0) REVERT: A 447 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8415 (ptpp) outliers start: 42 outliers final: 29 residues processed: 205 average time/residue: 0.1496 time to fit residues: 42.7775 Evaluate side-chains 207 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 382 THR Chi-restraints excluded: chain B residue 395 PHE 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 171 TRP Chi-restraints excluded: chain A residue 184 LEU 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 268 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 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 447 LYS 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: 0.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.080824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.071419 restraints weight = 35477.171| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 5.83 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6790 Z= 0.223 Angle : 0.909 14.115 9244 Z= 0.408 Chirality : 0.045 0.236 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.956 59.481 940 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.90 % Allowed : 28.23 % Favored : 65.87 % 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: 0.76 (0.29), residues: 876 helix: 1.35 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 392 HIS 0.005 0.001 HIS A 75 PHE 0.031 0.002 PHE A 153 TYR 0.043 0.002 TYR B 485 ARG 0.003 0.000 ARG A 431 *********************** 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 220 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.8001 (mp0) cc_final: 0.7743 (mp0) REVERT: B 171 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.7576 (m-90) REVERT: B 269 LEU cc_start: 0.8905 (tt) cc_final: 0.8679 (mt) REVERT: B 459 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6283 (mtmt) REVERT: B 472 ASP cc_start: 0.8817 (m-30) cc_final: 0.8553 (m-30) REVERT: A 154 LEU cc_start: 0.9481 (mt) cc_final: 0.9257 (mt) REVERT: A 171 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.7638 (m-90) REVERT: A 225 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6620 (mp) REVERT: A 271 MET cc_start: 0.7858 (ptt) cc_final: 0.7396 (ptt) REVERT: A 331 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: A 408 LEU cc_start: 0.8240 (mt) cc_final: 0.8022 (mt) REVERT: A 447 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8562 (ptpp) outliers start: 42 outliers final: 29 residues processed: 205 average time/residue: 0.1458 time to fit residues: 41.8709 Evaluate side-chains 209 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 382 THR 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 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 TRP Chi-restraints excluded: chain A residue 184 LEU 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 268 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 447 LYS 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: 6.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.081279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.071638 restraints weight = 34827.048| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 6.08 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6790 Z= 0.206 Angle : 0.913 15.019 9244 Z= 0.409 Chirality : 0.044 0.235 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.963 59.363 940 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.06 % Allowed : 30.48 % 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: 0.60 (0.28), residues: 876 helix: 1.23 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -2.72 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 392 HIS 0.005 0.001 HIS A 75 PHE 0.025 0.002 PHE A 153 TYR 0.045 0.002 TYR B 485 ARG 0.002 0.000 ARG A 431 *********************** 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 219 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLU cc_start: 0.8031 (mp0) cc_final: 0.7782 (mp0) REVERT: B 148 MET cc_start: 0.8382 (ptp) cc_final: 0.7859 (ptp) REVERT: B 393 ASP cc_start: 0.9648 (m-30) cc_final: 0.9383 (m-30) REVERT: B 456 TRP cc_start: 0.6695 (t-100) cc_final: 0.6415 (t-100) REVERT: B 459 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6284 (mtmt) REVERT: B 472 ASP cc_start: 0.8777 (m-30) cc_final: 0.8511 (m-30) REVERT: A 171 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7626 (m-90) REVERT: A 225 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6536 (mp) REVERT: A 271 MET cc_start: 0.7797 (ptt) cc_final: 0.7340 (ptt) REVERT: A 408 LEU cc_start: 0.8147 (mt) cc_final: 0.7894 (mt) REVERT: A 447 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (ptpp) outliers start: 36 outliers final: 27 residues processed: 205 average time/residue: 0.1490 time to fit residues: 42.6395 Evaluate side-chains 204 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain B residue 382 THR 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 122 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 TRP Chi-restraints excluded: chain A residue 184 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 268 THR 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 447 LYS 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: 0.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 19 optimal weight: 0.0020 chunk 73 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.083340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.073920 restraints weight = 35701.026| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 5.85 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6790 Z= 0.207 Angle : 0.955 14.777 9244 Z= 0.421 Chirality : 0.043 0.214 1136 Planarity : 0.004 0.045 1122 Dihedral : 5.927 57.909 940 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.63 % Allowed : 31.88 % 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: 0.67 (0.29), residues: 876 helix: 1.30 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.78 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 392 HIS 0.005 0.001 HIS A 75 PHE 0.023 0.001 PHE B 115 TYR 0.046 0.002 TYR B 485 ARG 0.002 0.000 ARG B 413 *********************** 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 211 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9056 (ttt) cc_final: 0.8822 (mmm) REVERT: B 107 GLU cc_start: 0.8094 (mp0) cc_final: 0.7849 (mp0) REVERT: B 456 TRP cc_start: 0.6675 (t-100) cc_final: 0.6376 (t-100) REVERT: B 459 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6167 (mtpp) REVERT: B 472 ASP cc_start: 0.8715 (m-30) cc_final: 0.8413 (m-30) REVERT: A 225 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6525 (mp) REVERT: A 271 MET cc_start: 0.7732 (ptt) cc_final: 0.7285 (ptt) REVERT: A 408 LEU cc_start: 0.8188 (mt) cc_final: 0.7930 (mt) REVERT: A 447 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8434 (ptpp) outliers start: 33 outliers final: 23 residues processed: 198 average time/residue: 0.1484 time to fit residues: 40.8511 Evaluate side-chains 194 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 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 396 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 447 LYS 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 13 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.082203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.072634 restraints weight = 36420.898| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.93 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6790 Z= 0.248 Angle : 1.011 15.665 9244 Z= 0.456 Chirality : 0.047 0.252 1136 Planarity : 0.004 0.045 1122 Dihedral : 6.009 58.622 940 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.93 % Allowed : 32.87 % Favored : 63.20 % 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: 0.48 (0.28), residues: 876 helix: 1.17 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.82 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 392 HIS 0.005 0.001 HIS A 75 PHE 0.021 0.002 PHE B 115 TYR 0.047 0.002 TYR B 485 ARG 0.008 0.000 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: 28 poor density : 170 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.9156 (ttt) cc_final: 0.8897 (mmm) REVERT: B 107 GLU cc_start: 0.8174 (mp0) cc_final: 0.7947 (mp0) REVERT: B 235 MET cc_start: 0.7716 (mpp) cc_final: 0.7097 (mpp) REVERT: B 459 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6329 (mtpp) REVERT: B 472 ASP cc_start: 0.8797 (m-30) cc_final: 0.8530 (m-30) REVERT: A 225 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 271 MET cc_start: 0.8101 (ptt) cc_final: 0.7587 (ptt) REVERT: A 408 LEU cc_start: 0.8193 (mt) cc_final: 0.7931 (mt) REVERT: A 447 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8564 (ptpp) outliers start: 28 outliers final: 20 residues processed: 189 average time/residue: 0.1384 time to fit residues: 37.2697 Evaluate side-chains 187 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 457 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 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 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 447 LYS 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: 9.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.081177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.071566 restraints weight = 35273.145| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 5.92 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6790 Z= 0.252 Angle : 1.050 21.030 9244 Z= 0.470 Chirality : 0.047 0.243 1136 Planarity : 0.005 0.045 1122 Dihedral : 6.098 59.664 940 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.93 % Allowed : 33.43 % Favored : 62.64 % 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: 0.36 (0.28), residues: 876 helix: 1.05 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.78 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 392 HIS 0.005 0.001 HIS A 75 PHE 0.023 0.002 PHE B 451 TYR 0.046 0.002 TYR B 485 ARG 0.005 0.000 ARG B 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.51 seconds wall clock time: 57 minutes 31.14 seconds (3451.14 seconds total)