Starting phenix.real_space_refine on Fri Oct 10 13:14:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6n_38992/10_2025/8y6n_38992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6n_38992/10_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_38992/10_2025/8y6n_38992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6n_38992/10_2025/8y6n_38992.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6n_38992/10_2025/8y6n_38992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6n_38992/10_2025/8y6n_38992_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.54, per 1000 atoms: 0.26 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: 0.49 Conformation dependent library (CDL) restraints added in 378.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 0.79 Time building geometry restraints manager: 0.66 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 388 TYR 0.013 0.002 TYR B 417 PHE 0.012 0.001 PHE B 382 TRP 0.017 0.003 TRP B 551 HIS 0.012 0.002 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00948 ( 5986) covalent geometry : angle 1.51702 ( 8132) hydrogen bonds : bond 0.28061 ( 242) hydrogen bonds : angle 10.17615 ( 690) *********************** 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 : 0.265 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: 0.6699 (mmm) REVERT: B 77 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6314 (mpt) REVERT: B 383 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8627 (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: 0.6624 (mmm) outliers start: 64 outliers final: 39 residues processed: 161 average time/residue: 0.0717 time to fit residues: 15.4932 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 : 0.365 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN B 354 GLN B 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.182516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161267 restraints weight = 7894.655| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.89 r_work: 0.3842 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5986 Z= 0.176 Angle : 0.748 9.297 8132 Z= 0.395 Chirality : 0.042 0.140 990 Planarity : 0.004 0.023 982 Dihedral : 12.362 83.475 889 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.04 % Favored : 90.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.29), residues: 752 helix: -1.42 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -2.30 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 339 TYR 0.009 0.001 TYR A 500 PHE 0.013 0.002 PHE A 66 TRP 0.008 0.001 TRP A 516 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5986) covalent geometry : angle 0.74785 ( 8132) hydrogen bonds : bond 0.05387 ( 242) hydrogen bonds : angle 5.80516 ( 690) *********************** 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 : 0.131 Fit side-chains REVERT: A 77 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6148 (mpt) REVERT: A 350 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 388 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.4053 (mmt180) REVERT: A 493 ASN cc_start: 0.6363 (m-40) cc_final: 0.6093 (m-40) REVERT: B 77 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6133 (mpt) REVERT: B 388 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.4084 (mmt180) REVERT: B 526 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6800 (pt0) outliers start: 44 outliers final: 23 residues processed: 140 average time/residue: 0.0741 time to fit residues: 13.6111 Evaluate side-chains 137 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 MET 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 350 LEU 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 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 MET 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 Chi-restraints excluded: chain B residue 526 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.0040 overall best weight: 0.1352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 493 ASN B 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.188183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168866 restraints weight = 7822.360| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.79 r_work: 0.3934 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5986 Z= 0.122 Angle : 0.703 17.141 8132 Z= 0.348 Chirality : 0.042 0.187 990 Planarity : 0.003 0.020 982 Dihedral : 10.356 80.348 854 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.98 % Favored : 91.76 % Rotamer: Outliers : 5.92 % Allowed : 17.60 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.29), residues: 752 helix: -1.10 (0.23), residues: 466 sheet: None (None), residues: 0 loop : -2.18 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 469 TYR 0.009 0.001 TYR A 500 PHE 0.010 0.001 PHE B 265 TRP 0.006 0.001 TRP B 29 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5986) covalent geometry : angle 0.70269 ( 8132) hydrogen bonds : bond 0.03839 ( 242) hydrogen bonds : angle 5.11608 ( 690) *********************** 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 154 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.239 Fit side-chains REVERT: A 45 MET cc_start: 0.5791 (tmm) cc_final: 0.5260 (tmm) REVERT: A 375 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: B 213 MET cc_start: 0.6307 (mtm) cc_final: 0.6090 (mtm) REVERT: B 375 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: B 411 MET cc_start: 0.7908 (mmt) cc_final: 0.7643 (mmt) REVERT: B 493 ASN cc_start: 0.5462 (m110) cc_final: 0.5204 (m-40) outliers start: 38 outliers final: 14 residues processed: 134 average time/residue: 0.0801 time to fit residues: 14.1136 Evaluate side-chains 120 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL 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 494 VAL 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 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 16 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.188471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168985 restraints weight = 7945.850| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.83 r_work: 0.3932 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2896 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= 0.119 Angle : 0.671 13.276 8132 Z= 0.330 Chirality : 0.040 0.139 990 Planarity : 0.003 0.023 982 Dihedral : 9.105 77.392 836 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.05 % Favored : 92.69 % Rotamer: Outliers : 4.83 % Allowed : 18.69 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.29), residues: 752 helix: -0.95 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.26 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.006 0.001 TYR A 500 PHE 0.021 0.001 PHE A 519 TRP 0.006 0.001 TRP A 516 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5986) covalent geometry : angle 0.67076 ( 8132) hydrogen bonds : bond 0.03546 ( 242) hydrogen bonds : angle 4.83986 ( 690) *********************** 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 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.211 Fit side-chains REVERT: A 375 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: A 411 MET cc_start: 0.8291 (mmt) cc_final: 0.8000 (mmt) REVERT: B 375 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6872 (mp10) outliers start: 31 outliers final: 20 residues processed: 120 average time/residue: 0.0776 time to fit residues: 12.5321 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 : 0.225 ------------------------------------------------------------------------------- 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 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 419 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 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 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4242 r_free = 0.4242 target = 0.187046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.167676 restraints weight = 8070.453| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.84 r_work: 0.3924 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5986 Z= 0.122 Angle : 0.654 12.038 8132 Z= 0.322 Chirality : 0.040 0.178 990 Planarity : 0.003 0.026 982 Dihedral : 8.832 76.508 836 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 4.98 % Allowed : 20.25 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.29), residues: 752 helix: -0.82 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.12 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.006 0.001 TYR A 500 PHE 0.018 0.001 PHE A 519 TRP 0.011 0.001 TRP A 523 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5986) covalent geometry : angle 0.65434 ( 8132) hydrogen bonds : bond 0.03226 ( 242) hydrogen bonds : angle 4.74737 ( 690) *********************** 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: 32 poor density : 109 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.5714 (tmm) cc_final: 0.5363 (tmm) REVERT: A 375 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6857 (mp10) REVERT: B 272 MET cc_start: 0.7396 (ttm) cc_final: 0.7094 (mmm) REVERT: B 375 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6879 (mp10) outliers start: 32 outliers final: 26 residues processed: 124 average time/residue: 0.0702 time to fit residues: 11.9631 Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 409 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 92 LEU 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 419 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.181712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.161794 restraints weight = 8035.154| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.85 r_work: 0.3868 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5986 Z= 0.168 Angle : 0.694 10.945 8132 Z= 0.343 Chirality : 0.041 0.159 990 Planarity : 0.003 0.030 982 Dihedral : 8.512 76.624 834 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.38 % Favored : 91.36 % Rotamer: Outliers : 6.07 % Allowed : 20.72 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.29), residues: 752 helix: -0.94 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -2.15 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.008 0.001 TYR B 413 PHE 0.027 0.001 PHE B 519 TRP 0.013 0.002 TRP A 523 HIS 0.008 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5986) covalent geometry : angle 0.69358 ( 8132) hydrogen bonds : bond 0.03309 ( 242) hydrogen bonds : angle 4.77116 ( 690) *********************** 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 146 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.6315 (tmm) cc_final: 0.5873 (tmm) REVERT: B 272 MET cc_start: 0.7314 (ttm) cc_final: 0.7110 (mmm) REVERT: B 375 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: B 522 LYS cc_start: 0.5857 (mmmt) cc_final: 0.5208 (mmmm) outliers start: 39 outliers final: 27 residues processed: 130 average time/residue: 0.0717 time to fit residues: 12.7157 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 419 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 92 LEU 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 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 Chi-restraints excluded: chain B residue 532 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 28 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.184500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165351 restraints weight = 8017.321| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.85 r_work: 0.3905 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3267 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= 0.132 Angle : 0.679 10.378 8132 Z= 0.333 Chirality : 0.041 0.206 990 Planarity : 0.003 0.027 982 Dihedral : 8.178 74.232 830 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.11 % Favored : 91.62 % Rotamer: Outliers : 5.45 % Allowed : 21.96 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.29), residues: 752 helix: -0.88 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -2.17 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.007 0.001 TYR B 500 PHE 0.018 0.001 PHE B 519 TRP 0.009 0.001 TRP A 363 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5986) covalent geometry : angle 0.67913 ( 8132) hydrogen bonds : bond 0.03207 ( 242) hydrogen bonds : angle 4.69523 ( 690) *********************** 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 140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.190 Fit side-chains REVERT: A 375 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: B 272 MET cc_start: 0.7494 (ttm) cc_final: 0.7241 (mmm) REVERT: B 375 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6852 (mp10) outliers start: 35 outliers final: 23 residues processed: 125 average time/residue: 0.0657 time to fit residues: 11.4941 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 399 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 463 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 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 51 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.180134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160407 restraints weight = 8055.466| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.84 r_work: 0.3845 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5986 Z= 0.179 Angle : 0.717 10.007 8132 Z= 0.354 Chirality : 0.043 0.196 990 Planarity : 0.003 0.030 982 Dihedral : 8.254 73.570 830 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.78 % Favored : 90.96 % Rotamer: Outliers : 4.98 % Allowed : 21.50 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.28), residues: 752 helix: -0.96 (0.22), residues: 480 sheet: None (None), residues: 0 loop : -2.19 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.009 0.001 TYR B 413 PHE 0.018 0.001 PHE A 66 TRP 0.014 0.002 TRP B 516 HIS 0.010 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5986) covalent geometry : angle 0.71744 ( 8132) hydrogen bonds : bond 0.03422 ( 242) hydrogen bonds : angle 4.82292 ( 690) *********************** 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 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.237 Fit side-chains REVERT: A 272 MET cc_start: 0.7183 (ttm) cc_final: 0.6925 (mmm) outliers start: 32 outliers final: 28 residues processed: 119 average time/residue: 0.0715 time to fit residues: 11.7248 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 418 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 463 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 286 MET Chi-restraints excluded: chain B residue 294 THR 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 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 463 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.0270 chunk 29 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.185375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.167601 restraints weight = 8034.817| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.66 r_work: 0.3941 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5986 Z= 0.120 Angle : 0.681 10.634 8132 Z= 0.332 Chirality : 0.040 0.182 990 Planarity : 0.003 0.025 982 Dihedral : 7.834 68.618 830 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 4.05 % Allowed : 22.74 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.29), residues: 752 helix: -0.67 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.005 0.001 TYR B 500 PHE 0.019 0.001 PHE B 519 TRP 0.009 0.001 TRP B 516 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5986) covalent geometry : angle 0.68053 ( 8132) hydrogen bonds : bond 0.03049 ( 242) hydrogen bonds : angle 4.66842 ( 690) *********************** 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 142 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.220 Fit side-chains REVERT: A 375 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: B 66 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6354 (m-10) outliers start: 26 outliers final: 20 residues processed: 127 average time/residue: 0.0709 time to fit residues: 12.4197 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 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 375 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.183234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165208 restraints weight = 8102.201| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.66 r_work: 0.3917 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3623 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= 0.125 Angle : 0.667 10.114 8132 Z= 0.326 Chirality : 0.041 0.182 990 Planarity : 0.003 0.028 982 Dihedral : 7.058 66.069 822 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 3.89 % Allowed : 22.74 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.29), residues: 752 helix: -0.55 (0.23), residues: 474 sheet: None (None), residues: 0 loop : -1.89 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.006 0.001 TYR A 500 PHE 0.018 0.001 PHE A 66 TRP 0.018 0.002 TRP B 363 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5986) covalent geometry : angle 0.66729 ( 8132) hydrogen bonds : bond 0.02994 ( 242) hydrogen bonds : angle 4.58959 ( 690) ********************** 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 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.218 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 120 average time/residue: 0.0663 time to fit residues: 11.2083 Evaluate side-chains 130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 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 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 272 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 375 GLN 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 463 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.182502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164764 restraints weight = 8037.112| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.64 r_work: 0.3911 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3668 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= 0.140 Angle : 0.684 9.892 8132 Z= 0.334 Chirality : 0.041 0.180 990 Planarity : 0.003 0.030 982 Dihedral : 6.965 61.636 822 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.42 % Rotamer: Outliers : 3.89 % Allowed : 22.74 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.30), residues: 752 helix: -0.53 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -1.85 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.006 0.001 TYR B 500 PHE 0.016 0.001 PHE A 66 TRP 0.022 0.002 TRP B 363 HIS 0.006 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5986) covalent geometry : angle 0.68391 ( 8132) hydrogen bonds : bond 0.03029 ( 242) hydrogen bonds : angle 4.58754 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.57 seconds wall clock time: 27 minutes 57.32 seconds (1677.32 seconds total)