Starting phenix.real_space_refine on Thu Jul 2 07:06:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wbx_37426/07_2026/8wbx_37426.cif" } resolution = 3.23 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= -0.002 sd= 0.052 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 44 5.16 5 C 4809 2.51 5 N 1202 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7331 At special positions: 0 Unit cell: (80.3, 94.6, 116.6, 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 44 16.00 O 1276 8.00 N 1202 7.00 C 4809 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: 0.47 Conformation dependent library (CDL) restraints added in 351.7 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.572A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.333A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.917A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.207A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 472 removed outlier: 3.678A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.810A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 4.509A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.691A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 581 through 594 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.794A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 380 through 406 removed outlier: 4.125A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 472 removed outlier: 3.705A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.907A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 4.547A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 4.076A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 512 through 541 Processing helix chain 'B' and resid 543 through 560 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.833A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.638A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.591A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.260A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 264 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 99 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.146A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1371 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: 0.77 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 1304 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7495 Sorted by residual: bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N TYR B 504 " pdb=" CA TYR B 504 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" N PHE A 275 " pdb=" CA PHE A 275 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N GLN B 593 " pdb=" CA GLN B 593 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 9896 1.81 - 3.61: 207 3.61 - 5.42: 45 5.42 - 7.22: 14 7.22 - 9.03: 3 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" C PHE B 583 " ideal model delta sigma weight residual 110.97 105.67 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" C PHE B 315 " ideal model delta sigma weight residual 111.36 106.34 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" C ASP B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta sigma weight residual 120.29 114.12 6.17 1.42e+00 4.96e-01 1.89e+01 angle pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O PHE B 583 " pdb=" C PHE B 583 " pdb=" N TYR B 584 " ideal model delta sigma weight residual 122.03 125.37 -3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3963 22.41 - 44.82: 375 44.82 - 67.23: 42 67.23 - 89.64: 3 89.64 - 112.04: 1 Dihedral angle restraints: 4384 sinusoidal: 1702 harmonic: 2682 Sorted by residual: dihedral pdb=" C10 A8S A 701 " pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " ideal model delta sinusoidal sigma weight residual 55.84 -56.20 112.04 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" CG ARG B 270 " pdb=" CD ARG B 270 " pdb=" NE ARG B 270 " pdb=" CZ ARG B 270 " ideal model delta sinusoidal sigma weight residual 180.00 135.10 44.90 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB MET B 274 " pdb=" CG MET B 274 " pdb=" SD MET B 274 " pdb=" CE MET B 274 " ideal model delta sinusoidal sigma weight residual -60.00 -119.79 59.79 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 954 0.047 - 0.095: 196 0.095 - 0.142: 43 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA PHE B 583 " pdb=" N PHE B 583 " pdb=" C PHE B 583 " pdb=" CB PHE B 583 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU A 652 " pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CB LEU A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1196 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 582 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR B 582 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 582 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 583 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 233 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2209 2.82 - 3.34: 7366 3.34 - 3.86: 12569 3.86 - 4.38: 13998 4.38 - 4.90: 23990 Nonbonded interactions: 60132 Sorted by model distance: nonbonded pdb=" O THR B 156 " pdb=" OG1 THR B 160 " model vdw 2.305 3.040 nonbonded pdb=" N ASP B 432 " pdb=" OD1 ASP B 432 " model vdw 2.368 3.120 nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 480 " model vdw 2.402 3.040 nonbonded pdb=" O LEU A 528 " pdb=" NH2 ARG A 650 " model vdw 2.410 3.120 nonbonded pdb=" O SER A 444 " pdb=" OH TYR A 526 " model vdw 2.424 3.040 ... (remaining 60127 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 90 through 660) 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.860 Find NCS groups from input model: 0.080 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 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 : 0.003 0.063 7495 Z= 0.178 Angle : 0.658 9.031 10165 Z= 0.351 Chirality : 0.040 0.236 1199 Planarity : 0.004 0.061 1242 Dihedral : 15.742 112.044 2660 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 22.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.29), residues: 918 helix: 2.00 (0.21), residues: 608 sheet: 0.12 (0.66), residues: 46 loop : -0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.026 0.001 TYR B 504 PHE 0.015 0.001 PHE A 499 TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.18 ( 7495) covalent geometry : angle 0.65759 / 0.35 (10165) hydrogen bonds : bond 0.12300 / 8.38 ( 467) hydrogen bonds : angle 4.95657 / 3.50 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.7843 (mt) cc_final: 0.7549 (mp) REVERT: A 506 MET cc_start: 0.6127 (mmp) cc_final: 0.5685 (ttt) REVERT: B 97 MET cc_start: 0.5764 (ttm) cc_final: 0.5536 (ttp) REVERT: B 569 VAL cc_start: 0.7387 (t) cc_final: 0.7135 (t) REVERT: B 575 TRP cc_start: 0.7253 (p-90) cc_final: 0.6630 (t-100) outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.0615 time to fit residues: 14.7100 Evaluate side-chains 150 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.0370 overall best weight: 0.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.194025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.169350 restraints weight = 9584.673| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.89 r_work: 0.4250 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7495 Z= 0.103 Angle : 0.558 9.001 10165 Z= 0.261 Chirality : 0.037 0.158 1199 Planarity : 0.004 0.053 1242 Dihedral : 4.878 89.893 1017 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.02 % Allowed : 21.66 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 918 helix: 2.16 (0.20), residues: 616 sheet: 0.19 (0.65), residues: 48 loop : -0.45 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.011 0.001 TYR B 298 PHE 0.022 0.001 PHE A 275 TRP 0.046 0.002 TRP B 575 HIS 0.003 0.000 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7495) covalent geometry : angle 0.55778 / 0.26 (10165) hydrogen bonds : bond 0.03181 / 2.09 ( 467) hydrogen bonds : angle 3.98723 / 2.81 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.170 Fit side-chains REVERT: A 252 LEU cc_start: 0.7906 (mt) cc_final: 0.7687 (mp) REVERT: A 310 MET cc_start: 0.8006 (ppp) cc_final: 0.7636 (ppp) REVERT: A 392 ILE cc_start: 0.7447 (mm) cc_final: 0.7200 (pt) REVERT: A 555 MET cc_start: 0.6067 (tpt) cc_final: 0.5821 (tpt) REVERT: A 568 LYS cc_start: 0.8041 (tttt) cc_final: 0.7712 (tttt) REVERT: A 652 LEU cc_start: 0.8445 (mm) cc_final: 0.7992 (tp) REVERT: B 161 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7065 (mm) REVERT: B 390 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6557 (tt) REVERT: B 635 MET cc_start: 0.6992 (mmm) cc_final: 0.6721 (tpp) REVERT: B 652 LEU cc_start: 0.8588 (mm) cc_final: 0.8112 (tp) outliers start: 24 outliers final: 9 residues processed: 178 average time/residue: 0.0589 time to fit residues: 14.7780 Evaluate side-chains 170 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.0030 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 overall best weight: 0.2886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 484 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.190300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.165618 restraints weight = 9776.040| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.85 r_work: 0.4207 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7495 Z= 0.095 Angle : 0.533 8.622 10165 Z= 0.246 Chirality : 0.037 0.144 1199 Planarity : 0.004 0.045 1242 Dihedral : 4.795 90.633 1016 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.40 % Allowed : 21.91 % Favored : 74.69 % 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 are not related in a simple way. whole: 1.97 (0.28), residues: 918 helix: 2.09 (0.20), residues: 628 sheet: 0.09 (0.63), residues: 48 loop : -0.52 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 410 TYR 0.008 0.001 TYR A 586 PHE 0.021 0.001 PHE A 275 TRP 0.019 0.001 TRP A 575 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 7495) covalent geometry : angle 0.53278 / 0.25 (10165) hydrogen bonds : bond 0.02789 / 1.82 ( 467) hydrogen bonds : angle 3.81940 / 2.69 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.224 Fit side-chains REVERT: A 159 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 310 MET cc_start: 0.8025 (ppp) cc_final: 0.7804 (ppp) REVERT: A 555 MET cc_start: 0.6257 (tpt) cc_final: 0.6016 (tpt) REVERT: A 652 LEU cc_start: 0.8547 (mm) cc_final: 0.8110 (tt) REVERT: B 161 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7108 (mm) REVERT: B 390 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6646 (tt) REVERT: B 462 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6645 (mt-10) REVERT: B 506 MET cc_start: 0.6528 (mmp) cc_final: 0.6048 (ttt) REVERT: B 568 LYS cc_start: 0.7773 (tttt) cc_final: 0.7539 (tttt) REVERT: B 652 LEU cc_start: 0.8565 (mm) cc_final: 0.8026 (tp) outliers start: 27 outliers final: 16 residues processed: 170 average time/residue: 0.0549 time to fit residues: 13.5025 Evaluate side-chains 164 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.183705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.157562 restraints weight = 10118.403| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.98 r_work: 0.4105 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7495 Z= 0.117 Angle : 0.541 8.718 10165 Z= 0.253 Chirality : 0.037 0.123 1199 Planarity : 0.004 0.045 1242 Dihedral : 4.660 86.609 1016 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.40 % Allowed : 22.54 % Favored : 74.06 % 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 are not related in a simple way. whole: 1.95 (0.28), residues: 918 helix: 2.13 (0.21), residues: 616 sheet: -0.24 (0.61), residues: 48 loop : -0.47 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.015 0.001 TYR A 475 PHE 0.022 0.002 PHE A 275 TRP 0.021 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7495) covalent geometry : angle 0.54120 / 0.25 (10165) hydrogen bonds : bond 0.02806 / 1.83 ( 467) hydrogen bonds : angle 3.86221 / 2.72 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.273 Fit side-chains REVERT: A 310 MET cc_start: 0.8181 (ppp) cc_final: 0.7944 (ppp) REVERT: A 392 ILE cc_start: 0.7585 (mm) cc_final: 0.7312 (tp) REVERT: A 555 MET cc_start: 0.6546 (tpt) cc_final: 0.6315 (tpt) REVERT: A 568 LYS cc_start: 0.8064 (tttt) cc_final: 0.7784 (tttt) REVERT: A 652 LEU cc_start: 0.8551 (mm) cc_final: 0.8097 (tt) REVERT: B 161 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7199 (mm) REVERT: B 273 GLN cc_start: 0.5905 (pp30) cc_final: 0.5402 (tp40) REVERT: B 310 MET cc_start: 0.8204 (ppp) cc_final: 0.7905 (ppp) REVERT: B 390 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6608 (tt) REVERT: B 424 MET cc_start: 0.6331 (mmm) cc_final: 0.6097 (mmt) REVERT: B 462 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6630 (mt-10) REVERT: B 652 LEU cc_start: 0.8572 (mm) cc_final: 0.8035 (tp) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 0.0499 time to fit residues: 12.3521 Evaluate side-chains 166 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.154835 restraints weight = 10110.950| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.97 r_work: 0.4083 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7495 Z= 0.114 Angle : 0.544 8.723 10165 Z= 0.251 Chirality : 0.038 0.124 1199 Planarity : 0.004 0.044 1242 Dihedral : 4.600 84.715 1016 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.65 % Allowed : 23.05 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.28), residues: 918 helix: 2.02 (0.20), residues: 614 sheet: -0.47 (0.61), residues: 48 loop : -0.54 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.014 0.001 TYR A 475 PHE 0.022 0.001 PHE A 275 TRP 0.024 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7495) covalent geometry : angle 0.54387 / 0.25 (10165) hydrogen bonds : bond 0.02772 / 1.81 ( 467) hydrogen bonds : angle 3.87564 / 2.73 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.258 Fit side-chains REVERT: A 273 GLN cc_start: 0.5879 (pp30) cc_final: 0.5596 (tp40) REVERT: A 310 MET cc_start: 0.8255 (ppp) cc_final: 0.7972 (ppp) REVERT: A 423 LEU cc_start: 0.7721 (tp) cc_final: 0.7396 (mp) REVERT: A 506 MET cc_start: 0.6294 (mmp) cc_final: 0.5482 (ttt) REVERT: A 555 MET cc_start: 0.6724 (tpt) cc_final: 0.6493 (tpt) REVERT: A 568 LYS cc_start: 0.8098 (tttt) cc_final: 0.7756 (tttt) REVERT: A 652 LEU cc_start: 0.8535 (mm) cc_final: 0.8072 (tt) REVERT: B 161 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7217 (mm) REVERT: B 310 MET cc_start: 0.8337 (ppp) cc_final: 0.7900 (ppp) REVERT: B 390 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6660 (tt) REVERT: B 462 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6553 (mt-10) REVERT: B 506 MET cc_start: 0.6649 (mmp) cc_final: 0.5994 (ttt) outliers start: 29 outliers final: 24 residues processed: 172 average time/residue: 0.0508 time to fit residues: 12.6015 Evaluate side-chains 177 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 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 = 0.4449 r_free = 0.4449 target = 0.176533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.150222 restraints weight = 10182.185| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.94 r_work: 0.4028 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7495 Z= 0.140 Angle : 0.584 8.735 10165 Z= 0.270 Chirality : 0.039 0.120 1199 Planarity : 0.004 0.044 1242 Dihedral : 4.652 82.264 1016 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.91 % Allowed : 23.17 % Favored : 71.91 % 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 are not related in a simple way. whole: 1.52 (0.28), residues: 918 helix: 1.84 (0.20), residues: 612 sheet: -0.92 (0.62), residues: 46 loop : -0.60 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 205 TYR 0.015 0.001 TYR B 475 PHE 0.023 0.002 PHE B 275 TRP 0.025 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7495) covalent geometry : angle 0.58441 / 0.27 (10165) hydrogen bonds : bond 0.03016 / 1.95 ( 467) hydrogen bonds : angle 4.00829 / 2.82 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.228 Fit side-chains REVERT: A 159 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6665 (tp30) REVERT: A 310 MET cc_start: 0.8341 (ppp) cc_final: 0.8044 (ppp) REVERT: A 387 PHE cc_start: 0.5982 (t80) cc_final: 0.5762 (t80) REVERT: A 482 MET cc_start: 0.7288 (mmt) cc_final: 0.6511 (mmm) REVERT: A 555 MET cc_start: 0.6796 (tpt) cc_final: 0.6582 (tpt) REVERT: A 568 LYS cc_start: 0.8054 (tttt) cc_final: 0.7740 (tttt) REVERT: A 635 MET cc_start: 0.6324 (tpp) cc_final: 0.6085 (tpt) REVERT: A 652 LEU cc_start: 0.8478 (mm) cc_final: 0.8019 (tt) REVERT: B 161 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7266 (mm) REVERT: B 310 MET cc_start: 0.8433 (ppp) cc_final: 0.7961 (ppp) REVERT: B 398 LEU cc_start: 0.7373 (mt) cc_final: 0.7046 (mt) REVERT: B 462 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6585 (mt-10) REVERT: B 506 MET cc_start: 0.6877 (mmp) cc_final: 0.6199 (ttt) REVERT: B 652 LEU cc_start: 0.8373 (mm) cc_final: 0.8057 (tp) outliers start: 39 outliers final: 29 residues processed: 179 average time/residue: 0.0609 time to fit residues: 15.2837 Evaluate side-chains 182 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.0050 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.177210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.151221 restraints weight = 10183.365| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.95 r_work: 0.4044 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7495 Z= 0.118 Angle : 0.576 9.734 10165 Z= 0.263 Chirality : 0.038 0.123 1199 Planarity : 0.004 0.048 1242 Dihedral : 4.629 82.040 1016 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.16 % Allowed : 23.93 % Favored : 71.91 % 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 are not related in a simple way. whole: 1.57 (0.28), residues: 918 helix: 1.91 (0.20), residues: 610 sheet: -1.02 (0.64), residues: 46 loop : -0.62 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 205 TYR 0.012 0.001 TYR A 475 PHE 0.021 0.002 PHE B 275 TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7495) covalent geometry : angle 0.57601 / 0.26 (10165) hydrogen bonds : bond 0.02845 / 1.85 ( 467) hydrogen bonds : angle 3.94099 / 2.78 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.226 Fit side-chains REVERT: A 310 MET cc_start: 0.8386 (ppp) cc_final: 0.8084 (ppp) REVERT: A 482 MET cc_start: 0.7312 (mmt) cc_final: 0.6522 (mmm) REVERT: A 506 MET cc_start: 0.6231 (mmp) cc_final: 0.5520 (ttt) REVERT: A 555 MET cc_start: 0.6750 (tpt) cc_final: 0.6545 (tpt) REVERT: A 568 LYS cc_start: 0.8094 (tttt) cc_final: 0.7784 (tttt) REVERT: A 635 MET cc_start: 0.6340 (tpp) cc_final: 0.6022 (tpt) REVERT: A 652 LEU cc_start: 0.8470 (mm) cc_final: 0.8017 (tt) REVERT: B 159 GLU cc_start: 0.7655 (tp30) cc_final: 0.7375 (tp30) REVERT: B 161 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7245 (mm) REVERT: B 291 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7830 (ttpp) REVERT: B 310 MET cc_start: 0.8400 (ppp) cc_final: 0.7896 (ppp) REVERT: B 392 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7644 (mm) REVERT: B 398 LEU cc_start: 0.7337 (mt) cc_final: 0.7009 (mt) REVERT: B 462 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6635 (mt-10) REVERT: B 506 MET cc_start: 0.6812 (mmp) cc_final: 0.6073 (ttt) REVERT: B 652 LEU cc_start: 0.8578 (mm) cc_final: 0.7977 (tp) outliers start: 33 outliers final: 25 residues processed: 174 average time/residue: 0.0618 time to fit residues: 15.2922 Evaluate side-chains 179 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 247 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.175716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.149654 restraints weight = 10206.385| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.95 r_work: 0.4022 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7495 Z= 0.128 Angle : 0.580 9.271 10165 Z= 0.268 Chirality : 0.038 0.122 1199 Planarity : 0.004 0.054 1242 Dihedral : 4.615 79.327 1016 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.03 % Allowed : 23.30 % Favored : 72.67 % 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 are not related in a simple way. whole: 1.51 (0.28), residues: 918 helix: 1.86 (0.20), residues: 612 sheet: -1.25 (0.63), residues: 46 loop : -0.59 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 205 TYR 0.013 0.001 TYR A 475 PHE 0.022 0.002 PHE B 275 TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7495) covalent geometry : angle 0.57994 / 0.27 (10165) hydrogen bonds : bond 0.02921 / 1.91 ( 467) hydrogen bonds : angle 3.99388 / 2.82 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.195 Fit side-chains REVERT: A 310 MET cc_start: 0.8392 (ppp) cc_final: 0.8064 (ppp) REVERT: A 506 MET cc_start: 0.6247 (mmp) cc_final: 0.5513 (ttt) REVERT: A 568 LYS cc_start: 0.8106 (tttt) cc_final: 0.7762 (tttt) REVERT: A 635 MET cc_start: 0.6372 (tpp) cc_final: 0.6012 (tpt) REVERT: A 652 LEU cc_start: 0.8469 (mm) cc_final: 0.8015 (tt) REVERT: B 161 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7200 (mm) REVERT: B 310 MET cc_start: 0.8424 (ppp) cc_final: 0.8196 (ppp) REVERT: B 398 LEU cc_start: 0.7332 (mt) cc_final: 0.7002 (mt) REVERT: B 462 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6490 (mt-10) REVERT: B 506 MET cc_start: 0.6827 (mmp) cc_final: 0.6143 (ttt) REVERT: B 652 LEU cc_start: 0.8504 (mm) cc_final: 0.7958 (tp) outliers start: 32 outliers final: 26 residues processed: 172 average time/residue: 0.0623 time to fit residues: 14.9365 Evaluate side-chains 178 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.175374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.149457 restraints weight = 10115.040| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.92 r_work: 0.4021 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7495 Z= 0.128 Angle : 0.597 8.953 10165 Z= 0.273 Chirality : 0.038 0.121 1199 Planarity : 0.004 0.055 1242 Dihedral : 4.593 78.398 1016 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.03 % Allowed : 24.18 % Favored : 71.79 % 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 are not related in a simple way. whole: 1.50 (0.28), residues: 918 helix: 1.89 (0.20), residues: 610 sheet: -1.33 (0.63), residues: 46 loop : -0.66 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 205 TYR 0.012 0.001 TYR A 475 PHE 0.022 0.002 PHE B 275 TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7495) covalent geometry : angle 0.59681 / 0.27 (10165) hydrogen bonds : bond 0.02891 / 1.89 ( 467) hydrogen bonds : angle 3.99026 / 2.81 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.192 Fit side-chains REVERT: A 310 MET cc_start: 0.8448 (ppp) cc_final: 0.8119 (ppp) REVERT: A 482 MET cc_start: 0.6963 (mmt) cc_final: 0.6468 (mmm) REVERT: A 506 MET cc_start: 0.6413 (mmp) cc_final: 0.5584 (ttt) REVERT: A 568 LYS cc_start: 0.8134 (tttt) cc_final: 0.7762 (tttt) REVERT: A 635 MET cc_start: 0.6454 (tpp) cc_final: 0.6038 (tpt) REVERT: A 652 LEU cc_start: 0.8479 (mm) cc_final: 0.8029 (tt) REVERT: B 161 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 310 MET cc_start: 0.8455 (ppp) cc_final: 0.7940 (ppp) REVERT: B 398 LEU cc_start: 0.7338 (mt) cc_final: 0.7010 (mt) REVERT: B 462 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6514 (mt-10) REVERT: B 506 MET cc_start: 0.6796 (mmp) cc_final: 0.6141 (ttt) REVERT: B 635 MET cc_start: 0.6926 (mmm) cc_final: 0.6536 (tpt) REVERT: B 652 LEU cc_start: 0.8511 (mm) cc_final: 0.7960 (tp) outliers start: 32 outliers final: 28 residues processed: 172 average time/residue: 0.0587 time to fit residues: 14.1571 Evaluate side-chains 178 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 14 optimal weight: 0.0060 chunk 73 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 247 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.178968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153167 restraints weight = 10083.129| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.95 r_work: 0.4071 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7495 Z= 0.103 Angle : 0.588 8.888 10165 Z= 0.268 Chirality : 0.037 0.127 1199 Planarity : 0.004 0.054 1242 Dihedral : 4.454 76.342 1016 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 25.06 % Favored : 72.29 % 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 are not related in a simple way. whole: 1.67 (0.28), residues: 918 helix: 2.00 (0.20), residues: 612 sheet: -1.20 (0.64), residues: 46 loop : -0.58 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 205 TYR 0.010 0.001 TYR A 475 PHE 0.020 0.001 PHE B 275 TRP 0.021 0.001 TRP A 575 HIS 0.003 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 7495) covalent geometry : angle 0.58764 / 0.27 (10165) hydrogen bonds : bond 0.02686 / 1.76 ( 467) hydrogen bonds : angle 3.84010 / 2.71 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.191 Fit side-chains REVERT: A 310 MET cc_start: 0.8435 (ppp) cc_final: 0.8112 (ppp) REVERT: A 482 MET cc_start: 0.6933 (mmt) cc_final: 0.6424 (mmm) REVERT: A 506 MET cc_start: 0.6367 (mmp) cc_final: 0.5610 (ttt) REVERT: A 568 LYS cc_start: 0.8137 (tttt) cc_final: 0.7784 (tttt) REVERT: A 652 LEU cc_start: 0.8411 (mm) cc_final: 0.8077 (tt) REVERT: B 161 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7189 (mm) REVERT: B 310 MET cc_start: 0.8392 (ppp) cc_final: 0.7881 (ppp) REVERT: B 398 LEU cc_start: 0.7262 (mt) cc_final: 0.6950 (mt) REVERT: B 462 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6641 (mt-10) REVERT: B 482 MET cc_start: 0.6954 (mmt) cc_final: 0.6481 (mmm) REVERT: B 506 MET cc_start: 0.6668 (mmp) cc_final: 0.6025 (ttt) REVERT: B 598 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7314 (mp0) REVERT: B 635 MET cc_start: 0.6952 (mmm) cc_final: 0.6582 (tpt) REVERT: B 652 LEU cc_start: 0.8491 (mm) cc_final: 0.7945 (tp) outliers start: 21 outliers final: 18 residues processed: 163 average time/residue: 0.0582 time to fit residues: 13.1955 Evaluate side-chains 167 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 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 = 0.4469 r_free = 0.4469 target = 0.178793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.153005 restraints weight = 10075.949| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.94 r_work: 0.4063 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7495 Z= 0.111 Angle : 0.589 8.715 10165 Z= 0.267 Chirality : 0.037 0.125 1199 Planarity : 0.005 0.064 1242 Dihedral : 4.376 72.325 1016 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.02 % Allowed : 25.06 % Favored : 71.91 % 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 are not related in a simple way. whole: 1.61 (0.28), residues: 918 helix: 1.94 (0.21), residues: 612 sheet: -1.26 (0.64), residues: 46 loop : -0.57 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 205 TYR 0.011 0.001 TYR A 475 PHE 0.019 0.001 PHE A 387 TRP 0.020 0.001 TRP A 575 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7495) covalent geometry : angle 0.58931 / 0.27 (10165) hydrogen bonds : bond 0.02703 / 1.77 ( 467) hydrogen bonds : angle 3.88114 / 2.75 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.47 seconds wall clock time: 25 minutes 40.91 seconds (1540.91 seconds total)