Starting phenix.real_space_refine on Thu Jun 5 09:33:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6n_38992/06_2025/8y6n_38992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6n_38992/06_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_38992/06_2025/8y6n_38992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6n_38992/06_2025/8y6n_38992.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6n_38992/06_2025/8y6n_38992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6n_38992/06_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-5710/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: 4.19, per 1000 atoms: 0.72 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: 1.53 Conformation dependent library (CDL) restraints added in 853.7 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: 0.56 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: 1.41 Time building geometry restraints manager: 1.75 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- 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= 0.657 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 Details of bonding type rmsd hydrogen bonds : bond 0.28061 ( 242) hydrogen bonds : angle 10.17615 ( 690) covalent geometry : bond 0.00948 ( 5986) covalent geometry : angle 1.51702 ( 8132) *********************** 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 : 0.650 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: 0.2037 time to fit residues: 43.1219 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 : 0.834 ------------------------------------------------------------------------------- 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 = 0.163362 restraints weight = 7736.946| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.85 r_work: 0.3868 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.87 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= 0.158 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 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 242) hydrogen bonds : angle 5.66276 ( 690) covalent geometry : bond 0.00337 ( 5986) covalent geometry : angle 0.74032 ( 8132) *********************** 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 : 1.017 Fit side-chains REVERT: A 388 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.4069 (mmt180) REVERT: A 493 ASN cc_start: 0.6089 (m110) cc_final: 0.5808 (m-40) REVERT: B 375 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: B 388 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.4016 (mmt180) REVERT: B 493 ASN cc_start: 0.6351 (m-40) cc_final: 0.6099 (m-40) outliers start: 44 outliers final: 22 residues processed: 142 average time/residue: 0.2246 time to fit residues: 41.8172 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 : 0.784 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.182578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162532 restraints weight = 7974.379| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.82 r_work: 0.3865 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2473 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= 0.153 Angle : 0.730 16.346 8132 Z= 0.360 Chirality : 0.042 0.189 990 Planarity : 0.003 0.021 982 Dihedral : 10.100 78.835 845 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.78 % Favored : 90.96 % Rotamer: Outliers : 5.14 % Allowed : 18.85 % Favored : 76.01 % 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: -2.41 (0.29), residues: 752 helix: -1.22 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.09 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 523 HIS 0.006 0.001 HIS A 389 PHE 0.013 0.001 PHE A 66 TYR 0.009 0.001 TYR A 500 ARG 0.002 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 242) hydrogen bonds : angle 5.19338 ( 690) covalent geometry : bond 0.00346 ( 5986) covalent geometry : angle 0.72978 ( 8132) *********************** 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 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.141 Fit side-chains REVERT: A 388 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.4593 (mmt180) REVERT: A 411 MET cc_start: 0.7879 (mmt) cc_final: 0.7669 (mmt) REVERT: B 45 MET cc_start: 0.5992 (tmm) cc_final: 0.5693 (tmm) REVERT: B 213 MET cc_start: 0.6409 (mtm) cc_final: 0.6148 (mtm) REVERT: B 375 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: B 388 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.4632 (mmt180) REVERT: B 411 MET cc_start: 0.8124 (mmt) cc_final: 0.7901 (mmt) outliers start: 33 outliers final: 18 residues processed: 129 average time/residue: 0.3126 time to fit residues: 54.3556 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.0170 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 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 = 0.4224 r_free = 0.4224 target = 0.185975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165701 restraints weight = 7973.494| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.88 r_work: 0.3904 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5986 Z= 0.124 Angle : 0.669 13.476 8132 Z= 0.331 Chirality : 0.040 0.151 990 Planarity : 0.003 0.021 982 Dihedral : 9.176 75.392 838 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.18 % Favored : 92.55 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.70 % 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: -2.26 (0.29), residues: 752 helix: -1.02 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 516 HIS 0.003 0.001 HIS B 389 PHE 0.021 0.001 PHE A 519 TYR 0.006 0.001 TYR A 500 ARG 0.005 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 242) hydrogen bonds : angle 4.85557 ( 690) covalent geometry : bond 0.00273 ( 5986) covalent geometry : angle 0.66884 ( 8132) *********************** 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 132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.635 Fit side-chains REVERT: A 375 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: B 66 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: B 213 MET cc_start: 0.6211 (mtm) cc_final: 0.5967 (mtm) REVERT: B 375 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6926 (mp10) outliers start: 27 outliers final: 19 residues processed: 117 average time/residue: 0.1794 time to fit residues: 27.5218 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 284 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 284 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.187994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168527 restraints weight = 7811.559| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.84 r_work: 0.3942 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5986 Z= 0.114 Angle : 0.646 12.263 8132 Z= 0.316 Chirality : 0.040 0.183 990 Planarity : 0.003 0.024 982 Dihedral : 8.435 73.540 836 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.31 % Favored : 92.42 % Rotamer: Outliers : 5.14 % Allowed : 19.31 % Favored : 75.55 % 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: -2.13 (0.29), residues: 752 helix: -0.88 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 523 HIS 0.004 0.001 HIS B 389 PHE 0.016 0.001 PHE A 519 TYR 0.006 0.001 TYR A 500 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 242) hydrogen bonds : angle 4.71478 ( 690) covalent geometry : bond 0.00243 ( 5986) covalent geometry : angle 0.64598 ( 8132) *********************** 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 142 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.622 Fit side-chains REVERT: A 375 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: B 45 MET cc_start: 0.5690 (tmm) cc_final: 0.5349 (tmm) REVERT: B 66 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5949 (m-10) REVERT: B 213 MET cc_start: 0.5991 (mtm) cc_final: 0.5787 (mtm) REVERT: B 272 MET cc_start: 0.7417 (ttm) cc_final: 0.7086 (mmm) REVERT: B 375 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6876 (mp10) outliers start: 33 outliers final: 20 residues processed: 128 average time/residue: 0.1549 time to fit residues: 26.8405 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 272 MET 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 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 294 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN 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: 1.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.184829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165523 restraints weight = 7889.472| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.79 r_work: 0.3908 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5986 Z= 0.141 Angle : 0.661 11.170 8132 Z= 0.325 Chirality : 0.040 0.161 990 Planarity : 0.003 0.027 982 Dihedral : 8.097 72.500 830 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.58 % Favored : 92.15 % Rotamer: Outliers : 6.07 % Allowed : 20.09 % Favored : 73.83 % 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: -2.07 (0.29), residues: 752 helix: -0.89 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -2.09 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 523 HIS 0.006 0.001 HIS B 389 PHE 0.020 0.001 PHE B 519 TYR 0.006 0.001 TYR A 500 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 242) hydrogen bonds : angle 4.69637 ( 690) covalent geometry : bond 0.00326 ( 5986) covalent geometry : angle 0.66060 ( 8132) *********************** 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 144 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.639 Fit side-chains REVERT: A 375 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: A 411 MET cc_start: 0.8372 (mmt) cc_final: 0.8022 (mmt) REVERT: B 66 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5957 (m-10) REVERT: B 213 MET cc_start: 0.6174 (mtm) cc_final: 0.5961 (mtm) REVERT: B 272 MET cc_start: 0.7462 (ttm) cc_final: 0.7186 (mmm) REVERT: B 375 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6883 (mp10) outliers start: 39 outliers final: 28 residues processed: 125 average time/residue: 0.1438 time to fit residues: 24.6718 Evaluate side-chains 134 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 272 MET 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 529 LEU 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 349 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 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 = 0.4199 r_free = 0.4199 target = 0.182990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164261 restraints weight = 7951.666| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.70 r_work: 0.3907 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5986 Z= 0.143 Angle : 0.659 10.664 8132 Z= 0.326 Chirality : 0.040 0.147 990 Planarity : 0.003 0.028 982 Dihedral : 8.028 70.427 830 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.71 % Favored : 92.02 % Rotamer: Outliers : 6.54 % Allowed : 19.78 % Favored : 73.68 % 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: -2.08 (0.29), residues: 752 helix: -0.89 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.12 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 523 HIS 0.006 0.001 HIS B 389 PHE 0.016 0.001 PHE B 519 TYR 0.008 0.001 TYR A 500 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 242) hydrogen bonds : angle 4.66066 ( 690) covalent geometry : bond 0.00337 ( 5986) covalent geometry : angle 0.65911 ( 8132) *********************** 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 148 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.560 Fit side-chains REVERT: A 362 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 375 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: B 66 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5911 (m-10) REVERT: B 272 MET cc_start: 0.7221 (ttm) cc_final: 0.6980 (mmm) REVERT: B 375 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: B 522 LYS cc_start: 0.6249 (mmmt) cc_final: 0.5459 (mmmm) outliers start: 42 outliers final: 30 residues processed: 129 average time/residue: 0.1783 time to fit residues: 31.4243 Evaluate side-chains 132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 272 MET 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 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 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 349 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 375 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4208 r_free = 0.4208 target = 0.183980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165006 restraints weight = 7886.788| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.78 r_work: 0.3897 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5986 Z= 0.136 Angle : 0.679 10.172 8132 Z= 0.330 Chirality : 0.042 0.217 990 Planarity : 0.003 0.028 982 Dihedral : 7.767 67.292 828 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.11 % Favored : 91.76 % Rotamer: Outliers : 6.23 % Allowed : 19.94 % Favored : 73.83 % 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: -2.06 (0.29), residues: 752 helix: -0.86 (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 0.011 0.001 TRP A 516 HIS 0.005 0.001 HIS B 389 PHE 0.016 0.001 PHE B 66 TYR 0.007 0.001 TYR B 500 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 242) hydrogen bonds : angle 4.70792 ( 690) covalent geometry : bond 0.00318 ( 5986) covalent geometry : angle 0.67909 ( 8132) *********************** 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 141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.626 Fit side-chains REVERT: B 66 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.6063 (m-10) REVERT: B 272 MET cc_start: 0.7203 (ttm) cc_final: 0.6966 (mmm) outliers start: 40 outliers final: 31 residues processed: 121 average time/residue: 0.1423 time to fit residues: 23.7955 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 : 0.586 ------------------------------------------------------------------------------- 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 272 MET 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 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 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 349 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 375 GLN 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: 0.4980 chunk 28 optimal weight: 0.0010 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.183900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165950 restraints weight = 7923.192| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.65 r_work: 0.3930 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5986 Z= 0.125 Angle : 0.678 9.932 8132 Z= 0.326 Chirality : 0.041 0.218 990 Planarity : 0.003 0.028 982 Dihedral : 7.360 63.889 826 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.61 % Allowed : 20.09 % Favored : 74.30 % 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: -1.95 (0.29), residues: 752 helix: -0.75 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.13 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 363 HIS 0.004 0.001 HIS B 389 PHE 0.017 0.001 PHE B 66 TYR 0.006 0.001 TYR A 500 ARG 0.001 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 242) hydrogen bonds : angle 4.71239 ( 690) covalent geometry : bond 0.00292 ( 5986) covalent geometry : angle 0.67753 ( 8132) *********************** 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 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.641 Fit side-chains REVERT: A 44 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5551 (mp) REVERT: B 66 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.6078 (m-10) REVERT: B 272 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6965 (mmm) REVERT: B 383 MET cc_start: 0.8314 (mmm) cc_final: 0.8083 (mmt) REVERT: B 522 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6175 (mmmt) outliers start: 36 outliers final: 30 residues processed: 127 average time/residue: 0.1381 time to fit residues: 24.2796 Evaluate side-chains 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 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 399 THR Chi-restraints excluded: chain A residue 409 VAL 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 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 272 MET 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 349 VAL Chi-restraints excluded: chain B residue 375 GLN 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 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: 3.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.0050 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.184273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.166728 restraints weight = 7944.897| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.65 r_work: 0.3928 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5986 Z= 0.122 Angle : 0.667 10.356 8132 Z= 0.322 Chirality : 0.041 0.216 990 Planarity : 0.003 0.029 982 Dihedral : 7.042 59.069 824 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.98 % Allowed : 20.40 % 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: -1.64 (0.29), residues: 752 helix: -0.54 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -1.93 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 363 HIS 0.004 0.001 HIS B 389 PHE 0.016 0.001 PHE B 519 TYR 0.006 0.001 TYR A 500 ARG 0.002 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 242) hydrogen bonds : angle 4.62099 ( 690) covalent geometry : bond 0.00288 ( 5986) covalent geometry : angle 0.66677 ( 8132) ********************** 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 139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.632 Fit side-chains REVERT: A 285 VAL cc_start: 0.6887 (t) cc_final: 0.6682 (t) REVERT: B 66 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5960 (m-10) REVERT: B 522 LYS cc_start: 0.6489 (mmmt) cc_final: 0.6226 (mmmt) outliers start: 32 outliers final: 28 residues processed: 123 average time/residue: 0.1339 time to fit residues: 22.9977 Evaluate side-chains 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 272 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 409 VAL 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 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 350 LEU Chi-restraints excluded: chain B residue 375 GLN 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 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 66 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.0170 chunk 68 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.186392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.169206 restraints weight = 8007.939| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.64 r_work: 0.3961 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3835 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= 0.114 Angle : 0.663 9.634 8132 Z= 0.318 Chirality : 0.041 0.211 990 Planarity : 0.003 0.029 982 Dihedral : 6.515 56.221 822 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.83 % Allowed : 21.18 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 752 helix: -0.36 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 363 HIS 0.003 0.001 HIS B 389 PHE 0.015 0.001 PHE B 519 TYR 0.005 0.001 TYR B 500 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 242) hydrogen bonds : angle 4.60287 ( 690) covalent geometry : bond 0.00264 ( 5986) covalent geometry : angle 0.66340 ( 8132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.39 seconds wall clock time: 60 minutes 0.51 seconds (3600.51 seconds total)