Starting phenix.real_space_refine on Tue Jan 14 06:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6n_38992/01_2025/8y6n_38992_neut.cif" } resolution = 3.4 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= -0.000 sd= 0.063 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 50 5.16 5 C 3860 2.51 5 N 938 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5858 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2929 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 3 Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2929 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 3 Time building chain proxies: 3.46, per 1000 atoms: 0.59 Number of scatterers: 5858 At special positions: 0 Unit cell: (102.837, 61.7025, 74.6925, 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 50 16.00 O 1010 8.00 N 938 7.00 C 3860 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: 1.41 Conformation dependent library (CDL) restraints added in 852.2 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 60.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.771A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 4.121A pdb=" N LEU A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.537A pdb=" N ILE A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 234 removed outlier: 3.802A pdb=" N GLY A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.250A pdb=" N VAL A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.651A pdb=" N VAL A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.597A pdb=" N LEU A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.031A pdb=" N ASN A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.941A pdb=" N GLU A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 5.533A pdb=" N VAL A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.573A pdb=" N ALA A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.627A pdb=" N SER A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.789A pdb=" N VAL A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 468 " --> pdb=" O CYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.576A pdb=" N PHE A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.771A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 4.121A pdb=" N LEU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 93 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 3.523A pdb=" N ILE B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 234 removed outlier: 3.802A pdb=" N GLY B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 removed outlier: 4.250A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.651A pdb=" N VAL B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.597A pdb=" N LEU B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 283 " --> pdb=" O GLY B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 285 through 293 removed outlier: 4.031A pdb=" N ASN B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 removed outlier: 3.941A pdb=" N GLU B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 5.533A pdb=" N VAL B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 removed outlier: 3.573A pdb=" N ALA B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.627A pdb=" N SER B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.789A pdb=" N VAL B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 468 " --> pdb=" O CYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 531 through 538 Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.577A pdb=" N PHE B 543 " --> pdb=" O LEU B 540 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 690 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: 1.47 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 874 1.30 - 1.43: 1594 1.43 - 1.55: 3428 1.55 - 1.68: 2 1.68 - 1.81: 88 Bond restraints: 5986 Sorted by residual: bond pdb=" CA SER A 387 " pdb=" CB SER A 387 " ideal model delta sigma weight residual 1.537 1.439 0.098 1.41e-02 5.03e+03 4.81e+01 bond pdb=" CA SER B 387 " pdb=" CB SER B 387 " ideal model delta sigma weight residual 1.537 1.440 0.097 1.41e-02 5.03e+03 4.74e+01 bond pdb=" CA SER B 402 " pdb=" CB SER B 402 " ideal model delta sigma weight residual 1.530 1.431 0.099 1.69e-02 3.50e+03 3.45e+01 bond pdb=" CA SER A 402 " pdb=" CB SER A 402 " ideal model delta sigma weight residual 1.530 1.431 0.099 1.69e-02 3.50e+03 3.42e+01 bond pdb=" C PRO A 415 " pdb=" O PRO A 415 " ideal model delta sigma weight residual 1.240 1.175 0.065 1.12e-02 7.97e+03 3.36e+01 ... (remaining 5981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 7654 3.05 - 6.10: 392 6.10 - 9.15: 59 9.15 - 12.20: 21 12.20 - 15.25: 6 Bond angle restraints: 8132 Sorted by residual: angle pdb=" N THR B 105 " pdb=" CA THR B 105 " pdb=" C THR B 105 " ideal model delta sigma weight residual 114.56 101.12 13.44 1.27e+00 6.20e-01 1.12e+02 angle pdb=" N THR A 105 " pdb=" CA THR A 105 " pdb=" C THR A 105 " ideal model delta sigma weight residual 114.56 101.17 13.39 1.27e+00 6.20e-01 1.11e+02 angle pdb=" N LYS A 528 " pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 113.88 101.91 11.97 1.23e+00 6.61e-01 9.47e+01 angle pdb=" N GLN B 549 " pdb=" CA GLN B 549 " pdb=" C GLN B 549 " ideal model delta sigma weight residual 113.30 101.61 11.69 1.34e+00 5.57e-01 7.62e+01 angle pdb=" N GLN A 549 " pdb=" CA GLN A 549 " pdb=" C GLN A 549 " ideal model delta sigma weight residual 113.30 101.62 11.68 1.34e+00 5.57e-01 7.59e+01 ... (remaining 8127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2989 17.86 - 35.73: 356 35.73 - 53.59: 96 53.59 - 71.46: 29 71.46 - 89.32: 12 Dihedral angle restraints: 3482 sinusoidal: 1284 harmonic: 2198 Sorted by residual: dihedral pdb=" C GLU B 362 " pdb=" N GLU B 362 " pdb=" CA GLU B 362 " pdb=" CB GLU B 362 " ideal model delta harmonic sigma weight residual -122.60 -105.54 -17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" C GLU A 362 " pdb=" N GLU A 362 " pdb=" CA GLU A 362 " pdb=" CB GLU A 362 " ideal model delta harmonic sigma weight residual -122.60 -105.55 -17.05 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C PRO B 336 " pdb=" N PRO B 336 " pdb=" CA PRO B 336 " pdb=" CB PRO B 336 " ideal model delta harmonic sigma weight residual -120.70 -106.59 -14.11 0 2.50e+00 1.60e-01 3.19e+01 ... (remaining 3479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 826 0.095 - 0.189: 93 0.189 - 0.284: 44 0.284 - 0.378: 16 0.378 - 0.473: 11 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA VAL B 74 " pdb=" N VAL B 74 " pdb=" C VAL B 74 " pdb=" CB VAL B 74 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA HIS B 389 " pdb=" N HIS B 389 " pdb=" C HIS B 389 " pdb=" CB HIS B 389 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 987 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 546 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C HIS A 546 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS A 546 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY A 547 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 546 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C HIS B 546 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS B 546 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY B 547 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 77 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET A 77 " -0.056 2.00e-02 2.50e+03 pdb=" O MET A 77 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 78 " 0.019 2.00e-02 2.50e+03 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 151 2.60 - 3.18: 5626 3.18 - 3.75: 8642 3.75 - 4.33: 12909 4.33 - 4.90: 20176 Nonbonded interactions: 47504 Sorted by model distance: nonbonded pdb=" CB LEU B 343 " pdb=" CG2 THR B 419 " model vdw 2.030 3.860 nonbonded pdb=" CB LEU A 343 " pdb=" CG2 THR A 419 " model vdw 2.030 3.860 nonbonded pdb=" CG LEU B 343 " pdb=" CG2 THR B 419 " model vdw 2.163 3.890 nonbonded pdb=" CG LEU A 343 " pdb=" CG2 THR A 419 " model vdw 2.164 3.890 nonbonded pdb=" O PHE A 519 " pdb=" OG SER A 520 " model vdw 2.293 3.040 ... (remaining 47499 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.009 0.099 5986 Z= 0.634 Angle : 1.517 15.252 8132 Z= 1.015 Chirality : 0.096 0.473 990 Planarity : 0.006 0.037 982 Dihedral : 18.060 89.321 2070 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 3.99 % Allowed : 14.36 % Favored : 81.65 % Rotamer: Outliers : 9.97 % Allowed : 14.17 % Favored : 75.86 % Cbeta Deviations : 1.98 % 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: -3.25 (0.30), residues: 752 helix: -1.72 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 551 HIS 0.012 0.002 HIS A 389 PHE 0.012 0.001 PHE B 382 TYR 0.013 0.002 TYR B 417 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.674 Fit side-chains REVERT: A 77 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6316 (mpt) REVERT: A 532 MET cc_start: 0.6985 (mmm) cc_final: 0.6700 (mmm) REVERT: B 77 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6315 (mpt) REVERT: B 383 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8626 (ttt) REVERT: B 525 LYS cc_start: 0.7841 (tmmt) cc_final: 0.7617 (ttpp) REVERT: B 532 MET cc_start: 0.6980 (mmm) cc_final: 0.6622 (mmm) outliers start: 64 outliers final: 40 residues processed: 161 average time/residue: 0.1627 time to fit residues: 34.7623 Evaluate side-chains 149 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 526 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 493 ASN B 354 GLN B 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.184161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163361 restraints weight = 7736.951| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.85 r_work: 0.3866 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5986 Z= 0.218 Angle : 0.740 9.248 8132 Z= 0.389 Chirality : 0.042 0.141 990 Planarity : 0.004 0.023 982 Dihedral : 12.263 82.870 891 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.38 % Favored : 91.09 % Rotamer: Outliers : 6.85 % Allowed : 16.36 % Favored : 76.79 % 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: -2.72 (0.29), residues: 752 helix: -1.39 (0.23), residues: 466 sheet: None (None), residues: 0 loop : -2.33 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 516 HIS 0.004 0.001 HIS A 389 PHE 0.012 0.001 PHE B 299 TYR 0.009 0.001 TYR A 500 ARG 0.004 0.001 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.597 Fit side-chains REVERT: A 388 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.4073 (mmt180) REVERT: A 493 ASN cc_start: 0.6087 (m110) cc_final: 0.5806 (m-40) REVERT: B 375 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: B 388 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.4020 (mmt180) REVERT: B 493 ASN cc_start: 0.6350 (m-40) cc_final: 0.6097 (m-40) outliers start: 44 outliers final: 22 residues processed: 142 average time/residue: 0.1694 time to fit residues: 31.5599 Evaluate side-chains 130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158928 restraints weight = 8008.858| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.81 r_work: 0.3829 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5986 Z= 0.302 Angle : 0.766 16.127 8132 Z= 0.381 Chirality : 0.044 0.192 990 Planarity : 0.004 0.024 982 Dihedral : 10.308 79.536 845 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.24 % Favored : 89.49 % Rotamer: Outliers : 5.14 % Allowed : 20.25 % Favored : 74.61 % 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: -2.56 (0.29), residues: 752 helix: -1.35 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -2.12 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 516 HIS 0.009 0.002 HIS B 389 PHE 0.014 0.001 PHE A 66 TYR 0.010 0.001 TYR A 500 ARG 0.003 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.583 Fit side-chains REVERT: A 375 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: A 388 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.4519 (mmt180) REVERT: A 411 MET cc_start: 0.7956 (mmt) cc_final: 0.7708 (mmt) REVERT: B 45 MET cc_start: 0.6065 (tmm) cc_final: 0.5721 (tmm) REVERT: B 375 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: B 388 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.4471 (mmt180) outliers start: 33 outliers final: 18 residues processed: 125 average time/residue: 0.1849 time to fit residues: 29.9244 Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.183665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163200 restraints weight = 8018.971| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.86 r_work: 0.3872 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5986 Z= 0.189 Angle : 0.669 13.648 8132 Z= 0.330 Chirality : 0.041 0.133 990 Planarity : 0.003 0.021 982 Dihedral : 9.325 75.397 838 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.98 % Favored : 91.76 % Rotamer: Outliers : 5.76 % Allowed : 19.16 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.48 (0.28), residues: 752 helix: -1.17 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -2.34 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 523 HIS 0.004 0.001 HIS B 389 PHE 0.021 0.001 PHE A 66 TYR 0.007 0.001 TYR A 500 ARG 0.001 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.650 Fit side-chains REVERT: A 66 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6178 (m-10) REVERT: A 213 MET cc_start: 0.6456 (mtm) cc_final: 0.6219 (mtm) REVERT: A 375 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: A 388 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5089 (mmt180) REVERT: B 66 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6121 (m-10) REVERT: B 213 MET cc_start: 0.6429 (mtm) cc_final: 0.6188 (mtm) REVERT: B 339 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7513 (tpt-90) REVERT: B 375 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: B 493 ASN cc_start: 0.5987 (m110) cc_final: 0.5766 (m-40) outliers start: 37 outliers final: 22 residues processed: 130 average time/residue: 0.1834 time to fit residues: 30.8508 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 532 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.185403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165399 restraints weight = 7811.964| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.81 r_work: 0.3895 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5986 Z= 0.179 Angle : 0.650 12.752 8132 Z= 0.322 Chirality : 0.040 0.194 990 Planarity : 0.003 0.022 982 Dihedral : 8.928 73.356 838 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 4.36 % Allowed : 21.03 % Favored : 74.61 % 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: -2.19 (0.29), residues: 752 helix: -0.97 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 523 HIS 0.004 0.001 HIS A 389 PHE 0.017 0.001 PHE A 66 TYR 0.006 0.001 TYR A 500 ARG 0.001 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.645 Fit side-chains REVERT: A 66 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6198 (m-10) REVERT: A 213 MET cc_start: 0.6366 (mtm) cc_final: 0.6135 (mtm) REVERT: A 375 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: B 66 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.6059 (m-10) REVERT: B 213 MET cc_start: 0.6283 (mtm) cc_final: 0.6065 (mtm) REVERT: B 375 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6998 (mp10) outliers start: 28 outliers final: 18 residues processed: 125 average time/residue: 0.1870 time to fit residues: 30.3266 Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN B 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.181661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161585 restraints weight = 7712.129| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.84 r_work: 0.3875 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5986 Z= 0.212 Angle : 0.661 11.680 8132 Z= 0.327 Chirality : 0.040 0.161 990 Planarity : 0.003 0.027 982 Dihedral : 8.638 72.419 834 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.11 % Favored : 91.62 % Rotamer: Outliers : 5.30 % Allowed : 20.25 % Favored : 74.45 % 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: -2.22 (0.28), residues: 752 helix: -0.98 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -2.19 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 523 HIS 0.005 0.001 HIS A 389 PHE 0.021 0.001 PHE B 519 TYR 0.007 0.001 TYR A 500 ARG 0.004 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.577 Fit side-chains REVERT: A 66 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6281 (m-10) REVERT: A 213 MET cc_start: 0.6242 (mtm) cc_final: 0.5986 (mtm) REVERT: A 532 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6496 (mmt) REVERT: B 45 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5804 (tmm) REVERT: B 66 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6200 (m-10) REVERT: B 213 MET cc_start: 0.6131 (mtm) cc_final: 0.5904 (mtm) REVERT: B 272 MET cc_start: 0.7255 (ttm) cc_final: 0.6974 (mmm) REVERT: B 375 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: B 522 LYS cc_start: 0.6160 (mmmt) cc_final: 0.5504 (mmmm) outliers start: 34 outliers final: 25 residues processed: 125 average time/residue: 0.1642 time to fit residues: 27.3944 Evaluate side-chains 130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 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 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.183075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163113 restraints weight = 7933.887| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.86 r_work: 0.3880 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5986 Z= 0.216 Angle : 0.663 11.036 8132 Z= 0.326 Chirality : 0.040 0.139 990 Planarity : 0.003 0.028 982 Dihedral : 8.455 70.358 834 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.71 % Favored : 92.15 % Rotamer: Outliers : 6.70 % Allowed : 20.25 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.29), residues: 752 helix: -0.93 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -2.11 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 516 HIS 0.005 0.001 HIS A 389 PHE 0.018 0.001 PHE A 66 TYR 0.006 0.001 TYR B 500 ARG 0.002 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.568 Fit side-chains REVERT: A 45 MET cc_start: 0.6280 (tmm) cc_final: 0.5859 (tmm) REVERT: A 66 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: A 375 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: A 532 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6443 (mmt) REVERT: B 45 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5836 (tmm) REVERT: B 66 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6141 (m-10) REVERT: B 272 MET cc_start: 0.7264 (ttm) cc_final: 0.6959 (mmm) REVERT: B 375 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: B 532 MET cc_start: 0.6513 (mmt) cc_final: 0.6292 (mmt) outliers start: 43 outliers final: 25 residues processed: 129 average time/residue: 0.1659 time to fit residues: 29.1533 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 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 = 0.4209 r_free = 0.4209 target = 0.183692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165364 restraints weight = 7787.560| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.66 r_work: 0.3912 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5986 Z= 0.191 Angle : 0.674 10.509 8132 Z= 0.325 Chirality : 0.041 0.225 990 Planarity : 0.003 0.028 982 Dihedral : 8.209 67.476 834 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.61 % Allowed : 21.50 % Favored : 72.90 % 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: -2.02 (0.29), residues: 752 helix: -0.82 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.14 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 363 HIS 0.004 0.001 HIS A 389 PHE 0.018 0.001 PHE A 66 TYR 0.006 0.001 TYR B 500 ARG 0.002 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.603 Fit side-chains REVERT: A 45 MET cc_start: 0.6315 (tmm) cc_final: 0.5915 (tmm) REVERT: A 66 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: A 375 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: B 45 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5875 (tmm) REVERT: B 66 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.6119 (m-10) REVERT: B 272 MET cc_start: 0.7054 (ttm) cc_final: 0.6836 (mmm) REVERT: B 375 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 522 LYS cc_start: 0.5547 (mmmt) cc_final: 0.5219 (mmmt) outliers start: 36 outliers final: 27 residues processed: 122 average time/residue: 0.1561 time to fit residues: 25.7672 Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.182817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.164106 restraints weight = 7823.679| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.68 r_work: 0.3903 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5986 Z= 0.211 Angle : 0.677 10.310 8132 Z= 0.327 Chirality : 0.041 0.218 990 Planarity : 0.003 0.028 982 Dihedral : 7.966 63.610 832 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.61 % Allowed : 21.65 % Favored : 72.74 % 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: -1.98 (0.29), residues: 752 helix: -0.78 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.14 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 363 HIS 0.005 0.001 HIS A 389 PHE 0.018 0.001 PHE A 66 TYR 0.007 0.001 TYR A 500 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.650 Fit side-chains REVERT: A 45 MET cc_start: 0.6374 (tmm) cc_final: 0.5978 (tmm) REVERT: A 375 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: B 45 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5899 (tmm) REVERT: B 272 MET cc_start: 0.7123 (ttm) cc_final: 0.6904 (mmm) REVERT: B 375 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: B 388 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5635 (tpt-90) outliers start: 36 outliers final: 25 residues processed: 121 average time/residue: 0.1668 time to fit residues: 27.1078 Evaluate side-chains 129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.185002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166736 restraints weight = 7829.653| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.67 r_work: 0.3944 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5986 Z= 0.187 Angle : 0.674 10.364 8132 Z= 0.325 Chirality : 0.041 0.210 990 Planarity : 0.003 0.027 982 Dihedral : 7.377 58.214 828 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.21 % Allowed : 23.36 % Favored : 72.43 % 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: -1.60 (0.30), residues: 752 helix: -0.55 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 363 HIS 0.003 0.001 HIS A 389 PHE 0.020 0.001 PHE A 66 TYR 0.006 0.001 TYR B 500 ARG 0.001 0.000 ARG B 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.587 Fit side-chains REVERT: A 45 MET cc_start: 0.6244 (tmm) cc_final: 0.5843 (tmm) REVERT: B 45 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5802 (tmm) REVERT: B 350 LEU cc_start: 0.7923 (tp) cc_final: 0.7393 (tp) REVERT: B 375 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: B 388 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5852 (tpt-90) outliers start: 27 outliers final: 21 residues processed: 119 average time/residue: 0.1486 time to fit residues: 23.9418 Evaluate side-chains 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.185826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.167746 restraints weight = 7855.979| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.64 r_work: 0.3948 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5986 Z= 0.183 Angle : 0.655 10.010 8132 Z= 0.317 Chirality : 0.040 0.211 990 Planarity : 0.003 0.028 982 Dihedral : 6.893 55.840 826 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.89 % Allowed : 23.68 % Favored : 72.43 % 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: -1.57 (0.30), residues: 752 helix: -0.52 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 363 HIS 0.003 0.001 HIS A 389 PHE 0.019 0.001 PHE A 66 TYR 0.006 0.001 TYR B 500 ARG 0.002 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.27 seconds wall clock time: 54 minutes 50.91 seconds (3290.91 seconds total)