Starting phenix.real_space_refine on Sat Aug 23 03:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.map" model { file = "/net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jli_36398/08_2025/8jli_36398.cif" } resolution = 3.38 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= 0.017 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 70 5.16 5 C 6034 2.51 5 N 1524 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9248 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4612 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 570} Chain breaks: 1 Chain: "B" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4612 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 570} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UKX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UKX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.18 Number of scatterers: 9248 At special positions: 0 Unit cell: (137.78, 70.55, 120.35, 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 70 16.00 O 1620 8.00 N 1524 7.00 C 6034 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: 0.58 Conformation dependent library (CDL) restraints added in 224.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 69.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.865A pdb=" N ALA A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 205 through 230 removed outlier: 4.348A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.343A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.606A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.503A pdb=" N GLY A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.889A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.605A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 444 through 482 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 592 through 623 removed outlier: 4.178A pdb=" N MET A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 5.410A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.786A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 705 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.757A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 162 through 183 removed outlier: 3.897A pdb=" N ALA B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 208 through 230 removed outlier: 3.814A pdb=" N PHE B 220 " --> pdb=" O MET B 216 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 252 Processing helix chain 'B' and resid 255 through 271 removed outlier: 4.358A pdb=" N GLY B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.592A pdb=" N ILE B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.509A pdb=" N HIS B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 removed outlier: 4.210A pdb=" N MET B 301 " --> pdb=" O CYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.887A pdb=" N VAL B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 357 through 364 removed outlier: 3.625A pdb=" N PHE B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 386 Processing helix chain 'B' and resid 422 through 439 removed outlier: 3.548A pdb=" N PHE B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 483 Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 592 through 623 removed outlier: 4.186A pdb=" N MET B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Proline residue: B 610 - end of helix removed outlier: 5.323A pdb=" N ASP B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 642 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 647 through 676 removed outlier: 3.770A pdb=" N ILE B 663 " --> pdb=" O GLY B 659 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 705 Processing helix chain 'B' and resid 712 through 731 removed outlier: 3.762A pdb=" N ILE B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 496 removed outlier: 6.116A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN A 513 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 495 " --> pdb=" O ASN A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 566 through 567 removed outlier: 5.906A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N PHE A 545 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 524 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ARG A 547 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 526 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 539 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A 520 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER A 541 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 522 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 538 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR A 559 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR A 540 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AA5, first strand: chain 'B' and resid 485 through 496 removed outlier: 6.122A pdb=" N GLY B 509 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG B 491 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR B 511 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU B 493 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN B 513 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 495 " --> pdb=" O ASN B 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 566 through 567 removed outlier: 5.896A pdb=" N PHE B 546 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N PHE B 545 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 524 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ARG B 547 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE B 526 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 539 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG B 520 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER B 541 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS B 522 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 538 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 559 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR B 540 " --> pdb=" O THR B 559 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.76 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: 1435 1.30 - 1.44: 2841 1.44 - 1.58: 5104 1.58 - 1.71: 0 1.71 - 1.85: 112 Bond restraints: 9492 Sorted by residual: bond pdb=" C ARG B 483 " pdb=" N THR B 484 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.31e-02 5.83e+03 5.82e+01 bond pdb=" C ASP B 586 " pdb=" N VAL B 587 " ideal model delta sigma weight residual 1.332 1.246 0.086 1.15e-02 7.56e+03 5.65e+01 bond pdb=" C PHE A 439 " pdb=" N GLY A 440 " ideal model delta sigma weight residual 1.330 1.440 -0.109 1.49e-02 4.50e+03 5.39e+01 bond pdb=" C TYR B 443 " pdb=" N ARG B 444 " ideal model delta sigma weight residual 1.332 1.420 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C HIS B 387 " pdb=" O HIS B 387 " ideal model delta sigma weight residual 1.238 1.167 0.070 1.28e-02 6.10e+03 3.03e+01 ... (remaining 9487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 12765 3.82 - 7.64: 63 7.64 - 11.46: 5 11.46 - 15.27: 5 15.27 - 19.09: 2 Bond angle restraints: 12840 Sorted by residual: angle pdb=" CA HIS B 387 " pdb=" C HIS B 387 " pdb=" N PRO B 388 " ideal model delta sigma weight residual 118.44 99.35 19.09 1.59e+00 3.96e-01 1.44e+02 angle pdb=" CA HIS B 387 " pdb=" C HIS B 387 " pdb=" O HIS B 387 " ideal model delta sigma weight residual 120.16 136.18 -16.02 1.37e+00 5.33e-01 1.37e+02 angle pdb=" N PRO B 388 " pdb=" CA PRO B 388 " pdb=" CB PRO B 388 " ideal model delta sigma weight residual 103.25 93.39 9.86 1.05e+00 9.07e-01 8.81e+01 angle pdb=" O PHE A 439 " pdb=" C PHE A 439 " pdb=" N GLY A 440 " ideal model delta sigma weight residual 122.08 135.63 -13.55 1.46e+00 4.69e-01 8.61e+01 angle pdb=" CA PRO B 388 " pdb=" N PRO B 388 " pdb=" CD PRO B 388 " ideal model delta sigma weight residual 112.00 124.28 -12.28 1.40e+00 5.10e-01 7.70e+01 ... (remaining 12835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4977 16.54 - 33.08: 385 33.08 - 49.61: 73 49.61 - 66.15: 7 66.15 - 82.69: 12 Dihedral angle restraints: 5454 sinusoidal: 2120 harmonic: 3334 Sorted by residual: dihedral pdb=" N PRO B 388 " pdb=" C PRO B 388 " pdb=" CA PRO B 388 " pdb=" CB PRO B 388 " ideal model delta harmonic sigma weight residual 115.10 105.33 9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" CA THR B 395 " pdb=" C THR B 395 " pdb=" N HIS B 396 " pdb=" CA HIS B 396 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG A 483 " pdb=" C ARG A 483 " pdb=" N THR A 484 " pdb=" CA THR A 484 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 825 0.050 - 0.101: 426 0.101 - 0.151: 127 0.151 - 0.201: 15 0.201 - 0.252: 7 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C6 UKX B 801 " pdb=" C5 UKX B 801 " pdb=" C7 UKX B 801 " pdb=" N1 UKX B 801 " both_signs ideal model delta sigma weight residual False 2.45 2.71 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU B 147 " pdb=" N GLU B 147 " pdb=" C GLU B 147 " pdb=" CB GLU B 147 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO A 274 " pdb=" N PRO A 274 " pdb=" C PRO A 274 " pdb=" CB PRO A 274 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1397 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 387 " 0.028 2.00e-02 2.50e+03 5.54e-02 3.07e+01 pdb=" C HIS B 387 " -0.096 2.00e-02 2.50e+03 pdb=" O HIS B 387 " 0.041 2.00e-02 2.50e+03 pdb=" N PRO B 388 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 277 " 0.064 2.00e-02 2.50e+03 4.16e-02 3.03e+01 pdb=" CG PHE A 277 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 277 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 277 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE A 277 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 277 " 0.027 2.00e-02 2.50e+03 pdb=" CZ PHE A 277 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 644 " -0.066 2.00e-02 2.50e+03 4.13e-02 2.98e+01 pdb=" CG PHE A 644 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 644 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 644 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE A 644 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 644 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 644 " -0.029 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 85 2.60 - 3.17: 7898 3.17 - 3.75: 14619 3.75 - 4.32: 20017 4.32 - 4.90: 34030 Nonbonded interactions: 76649 Sorted by model distance: nonbonded pdb=" OE1 GLU B 144 " pdb=" CD1 ILE B 400 " model vdw 2.021 3.460 nonbonded pdb=" OD1 ASP A 227 " pdb=" OG1 THR A 683 " model vdw 2.057 3.040 nonbonded pdb=" OD2 ASP B 227 " pdb=" OG1 THR B 684 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 279 " pdb=" O PRO B 355 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.245 3.040 ... (remaining 76644 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: 3.340 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 6.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 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 : 0.008 0.127 9492 Z= 0.529 Angle : 0.997 19.093 12840 Z= 0.645 Chirality : 0.063 0.252 1400 Planarity : 0.008 0.090 1616 Dihedral : 12.670 82.689 3326 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.09 % 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: 0.78 (0.24), residues: 1164 helix: 1.48 (0.19), residues: 760 sheet: 1.38 (1.40), residues: 20 loop : -1.52 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.003 ARG A 624 TYR 0.043 0.006 TYR A 212 PHE 0.066 0.006 PHE A 644 TRP 0.038 0.009 TRP B 166 HIS 0.018 0.003 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00832 ( 9492) covalent geometry : angle 0.99700 (12840) hydrogen bonds : bond 0.11820 ( 631) hydrogen bonds : angle 6.24150 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7460 (mtm-85) REVERT: A 152 TYR cc_start: 0.6937 (t80) cc_final: 0.6578 (t80) REVERT: A 213 LEU cc_start: 0.6986 (mt) cc_final: 0.6728 (tt) REVERT: A 465 THR cc_start: 0.7315 (m) cc_final: 0.7111 (m) REVERT: A 560 ASP cc_start: 0.6577 (p0) cc_final: 0.6261 (p0) REVERT: A 580 LYS cc_start: 0.6929 (mttm) cc_final: 0.6720 (mttt) REVERT: A 595 TYR cc_start: 0.5858 (m-80) cc_final: 0.5606 (t80) REVERT: A 626 ARG cc_start: 0.5447 (mmt180) cc_final: 0.4809 (mtt180) REVERT: A 742 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6875 (tm-30) REVERT: B 228 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8215 (mmm160) REVERT: B 286 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6858 (tt0) REVERT: B 376 GLN cc_start: 0.7247 (tt0) cc_final: 0.6910 (tp40) REVERT: B 471 MET cc_start: 0.7969 (mmm) cc_final: 0.7656 (tpp) REVERT: B 533 GLU cc_start: 0.6663 (mp0) cc_final: 0.6388 (tm-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.0873 time to fit residues: 25.9089 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 503 ASN B 242 ASN B 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.222440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170868 restraints weight = 10216.827| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.66 r_work: 0.4017 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9492 Z= 0.161 Angle : 0.570 6.456 12840 Z= 0.307 Chirality : 0.041 0.153 1400 Planarity : 0.004 0.029 1616 Dihedral : 4.715 36.677 1296 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.76 % Allowed : 7.46 % Favored : 89.78 % 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: 1.24 (0.25), residues: 1164 helix: 1.75 (0.18), residues: 766 sheet: -0.14 (0.42), residues: 160 loop : -1.51 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 334 TYR 0.023 0.002 TYR B 462 PHE 0.021 0.002 PHE A 245 TRP 0.011 0.001 TRP A 333 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9492) covalent geometry : angle 0.56984 (12840) hydrogen bonds : bond 0.05158 ( 631) hydrogen bonds : angle 4.94325 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7898 (mmm160) REVERT: A 145 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7376 (mtm-85) REVERT: A 367 HIS cc_start: 0.3161 (OUTLIER) cc_final: 0.2527 (t70) REVERT: A 465 THR cc_start: 0.7525 (m) cc_final: 0.7314 (m) REVERT: A 626 ARG cc_start: 0.5371 (mmt180) cc_final: 0.5091 (mtt180) REVERT: B 376 GLN cc_start: 0.7185 (tt0) cc_final: 0.6701 (tp40) REVERT: B 544 THR cc_start: 0.7439 (m) cc_final: 0.7237 (m) REVERT: B 641 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6743 (t80) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 0.0729 time to fit residues: 16.4340 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 367 HIS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 8 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 = 0.4639 r_free = 0.4639 target = 0.219820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168885 restraints weight = 10315.811| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.67 r_work: 0.4004 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9492 Z= 0.140 Angle : 0.532 6.682 12840 Z= 0.283 Chirality : 0.040 0.143 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.471 34.740 1296 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.04 % Allowed : 10.94 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.47 (0.25), residues: 1164 helix: 1.93 (0.18), residues: 768 sheet: 1.37 (1.35), residues: 20 loop : -1.09 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 228 TYR 0.017 0.001 TYR B 462 PHE 0.026 0.001 PHE A 245 TRP 0.014 0.001 TRP A 371 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9492) covalent geometry : angle 0.53200 (12840) hydrogen bonds : bond 0.04565 ( 631) hydrogen bonds : angle 4.54900 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7445 (mtm-85) REVERT: A 298 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5942 (mmm) REVERT: A 367 HIS cc_start: 0.3561 (OUTLIER) cc_final: 0.2910 (t70) REVERT: A 465 THR cc_start: 0.7509 (m) cc_final: 0.7292 (m) REVERT: A 626 ARG cc_start: 0.5513 (mmt180) cc_final: 0.5131 (mtt180) REVERT: B 202 SER cc_start: 0.8192 (t) cc_final: 0.7861 (p) REVERT: B 346 PHE cc_start: 0.6176 (m-10) cc_final: 0.5936 (t80) REVERT: B 376 GLN cc_start: 0.7394 (tt0) cc_final: 0.7028 (tp40) REVERT: B 451 MET cc_start: 0.7797 (mtm) cc_final: 0.7571 (mtp) REVERT: B 544 THR cc_start: 0.7453 (m) cc_final: 0.7210 (m) REVERT: B 641 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6892 (t80) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.0743 time to fit residues: 14.7507 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 367 HIS Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.220390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166834 restraints weight = 10528.379| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.82 r_work: 0.3953 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9492 Z= 0.139 Angle : 0.516 8.987 12840 Z= 0.273 Chirality : 0.039 0.137 1400 Planarity : 0.003 0.029 1616 Dihedral : 4.397 33.299 1296 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.76 % Allowed : 12.58 % Favored : 84.66 % 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 (0.25), residues: 1164 helix: 2.03 (0.18), residues: 768 sheet: 1.19 (1.37), residues: 20 loop : -1.10 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.014 0.001 TYR A 169 PHE 0.022 0.001 PHE A 686 TRP 0.014 0.001 TRP A 432 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9492) covalent geometry : angle 0.51635 (12840) hydrogen bonds : bond 0.04377 ( 631) hydrogen bonds : angle 4.36851 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 564 TYR cc_start: 0.6276 (p90) cc_final: 0.5981 (p90) REVERT: A 626 ARG cc_start: 0.5511 (mmt180) cc_final: 0.5104 (mtt180) REVERT: A 693 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7467 (t) REVERT: A 742 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6369 (tm-30) REVERT: B 202 SER cc_start: 0.8229 (t) cc_final: 0.7923 (p) REVERT: B 206 MET cc_start: 0.6708 (tpp) cc_final: 0.6468 (tpp) REVERT: B 451 MET cc_start: 0.7788 (mtm) cc_final: 0.7578 (mtp) outliers start: 27 outliers final: 19 residues processed: 143 average time/residue: 0.0671 time to fit residues: 13.8894 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.223950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171054 restraints weight = 10410.741| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.84 r_work: 0.3959 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9492 Z= 0.130 Angle : 0.519 11.227 12840 Z= 0.270 Chirality : 0.039 0.142 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.324 31.985 1296 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.07 % Allowed : 13.29 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.25), residues: 1164 helix: 2.14 (0.18), residues: 768 sheet: 1.15 (1.34), residues: 20 loop : -1.08 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.013 0.001 TYR B 462 PHE 0.021 0.001 PHE A 245 TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9492) covalent geometry : angle 0.51869 (12840) hydrogen bonds : bond 0.04213 ( 631) hydrogen bonds : angle 4.27267 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5469 (mmt180) cc_final: 0.5046 (mtt180) REVERT: A 693 CYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7335 (t) REVERT: A 742 GLN cc_start: 0.6920 (tm-30) cc_final: 0.6658 (tm-30) REVERT: B 202 SER cc_start: 0.8158 (t) cc_final: 0.7835 (p) REVERT: B 206 MET cc_start: 0.6789 (tpp) cc_final: 0.6559 (tpp) REVERT: B 451 MET cc_start: 0.7840 (mtm) cc_final: 0.7610 (mtp) REVERT: B 471 MET cc_start: 0.7679 (tpp) cc_final: 0.6945 (ttt) outliers start: 30 outliers final: 25 residues processed: 143 average time/residue: 0.0598 time to fit residues: 12.8430 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.0070 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.223775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.170845 restraints weight = 10444.628| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.83 r_work: 0.3921 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9492 Z= 0.124 Angle : 0.513 12.449 12840 Z= 0.267 Chirality : 0.039 0.174 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.220 30.289 1296 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.56 % Allowed : 14.52 % Favored : 82.92 % 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: 1.77 (0.25), residues: 1164 helix: 2.22 (0.18), residues: 768 sheet: 0.81 (1.28), residues: 20 loop : -1.08 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.014 0.001 TYR A 564 PHE 0.020 0.001 PHE A 245 TRP 0.010 0.001 TRP A 333 HIS 0.015 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9492) covalent geometry : angle 0.51345 (12840) hydrogen bonds : bond 0.04064 ( 631) hydrogen bonds : angle 4.20426 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5548 (mmt180) cc_final: 0.5136 (mtt180) REVERT: A 651 MET cc_start: 0.6954 (mmt) cc_final: 0.6447 (mmt) REVERT: A 693 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7356 (t) REVERT: A 742 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6624 (tm-30) REVERT: B 202 SER cc_start: 0.8100 (t) cc_final: 0.7779 (p) REVERT: B 206 MET cc_start: 0.6820 (tpp) cc_final: 0.6618 (tpp) REVERT: B 269 ILE cc_start: 0.6795 (tp) cc_final: 0.6587 (tp) REVERT: B 451 MET cc_start: 0.7925 (mtm) cc_final: 0.7717 (mtp) REVERT: B 494 HIS cc_start: 0.6907 (t-90) cc_final: 0.6650 (t-90) outliers start: 25 outliers final: 22 residues processed: 138 average time/residue: 0.0605 time to fit residues: 12.6687 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.218669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165307 restraints weight = 10595.387| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.73 r_work: 0.3857 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9492 Z= 0.182 Angle : 0.587 14.311 12840 Z= 0.304 Chirality : 0.041 0.190 1400 Planarity : 0.004 0.032 1616 Dihedral : 4.609 35.620 1296 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.97 % Allowed : 15.13 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.25), residues: 1164 helix: 1.98 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.19 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 262 TYR 0.017 0.002 TYR B 306 PHE 0.022 0.002 PHE A 245 TRP 0.014 0.001 TRP A 300 HIS 0.028 0.002 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9492) covalent geometry : angle 0.58729 (12840) hydrogen bonds : bond 0.04807 ( 631) hydrogen bonds : angle 4.38777 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5517 (mmt180) cc_final: 0.5089 (mtt180) REVERT: A 651 MET cc_start: 0.7149 (mmt) cc_final: 0.6474 (mmt) REVERT: A 693 CYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7356 (t) REVERT: B 206 MET cc_start: 0.7010 (tpp) cc_final: 0.6800 (tpp) REVERT: B 369 GLU cc_start: 0.6818 (pm20) cc_final: 0.6601 (pt0) REVERT: B 451 MET cc_start: 0.7956 (mtm) cc_final: 0.7658 (mtm) REVERT: B 494 HIS cc_start: 0.7105 (t-90) cc_final: 0.6876 (t-90) outliers start: 29 outliers final: 23 residues processed: 134 average time/residue: 0.0696 time to fit residues: 13.7870 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.216154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.164481 restraints weight = 10497.112| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.40 r_work: 0.3899 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9492 Z= 0.149 Angle : 0.565 15.140 12840 Z= 0.292 Chirality : 0.040 0.189 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.554 34.602 1296 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 16.26 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.25), residues: 1164 helix: 2.06 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 624 TYR 0.014 0.001 TYR B 306 PHE 0.021 0.002 PHE A 245 TRP 0.014 0.001 TRP A 300 HIS 0.005 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9492) covalent geometry : angle 0.56454 (12840) hydrogen bonds : bond 0.04473 ( 631) hydrogen bonds : angle 4.32243 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.7677 (m-80) cc_final: 0.7287 (m-80) REVERT: A 626 ARG cc_start: 0.5652 (mmt180) cc_final: 0.5130 (mtt180) REVERT: A 651 MET cc_start: 0.7050 (mmt) cc_final: 0.6400 (mmt) REVERT: A 693 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7549 (t) REVERT: B 206 MET cc_start: 0.7160 (tpp) cc_final: 0.6956 (tpp) REVERT: B 369 GLU cc_start: 0.6930 (pm20) cc_final: 0.6711 (pt0) REVERT: B 494 HIS cc_start: 0.7247 (t-90) cc_final: 0.7046 (t-90) REVERT: B 619 MET cc_start: 0.8242 (ttm) cc_final: 0.8029 (ttm) outliers start: 26 outliers final: 23 residues processed: 133 average time/residue: 0.0597 time to fit residues: 11.6835 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.0000 chunk 105 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.222552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.168685 restraints weight = 10388.762| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.94 r_work: 0.3942 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9492 Z= 0.123 Angle : 0.528 15.216 12840 Z= 0.271 Chirality : 0.039 0.213 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.244 29.998 1296 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.94 % Allowed : 16.97 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.25), residues: 1164 helix: 2.23 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 624 TYR 0.014 0.001 TYR A 564 PHE 0.019 0.001 PHE A 536 TRP 0.014 0.001 TRP A 300 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9492) covalent geometry : angle 0.52780 (12840) hydrogen bonds : bond 0.03968 ( 631) hydrogen bonds : angle 4.17281 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.5551 (mmm) cc_final: 0.3897 (mpp) REVERT: A 462 TYR cc_start: 0.7654 (m-80) cc_final: 0.7255 (m-80) REVERT: A 626 ARG cc_start: 0.5472 (mmt180) cc_final: 0.5035 (mtt180) REVERT: A 651 MET cc_start: 0.6906 (mmt) cc_final: 0.6332 (mmt) REVERT: B 269 ILE cc_start: 0.6694 (tp) cc_final: 0.6485 (tp) REVERT: B 619 MET cc_start: 0.8133 (ttm) cc_final: 0.7899 (ttm) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.0571 time to fit residues: 11.2522 Evaluate side-chains 128 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 636 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 79 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 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 = 0.4638 r_free = 0.4638 target = 0.220990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.167261 restraints weight = 10464.655| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.85 r_work: 0.3967 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9492 Z= 0.111 Angle : 0.523 15.886 12840 Z= 0.265 Chirality : 0.038 0.202 1400 Planarity : 0.003 0.035 1616 Dihedral : 4.016 26.115 1296 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.74 % Allowed : 17.18 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.25), residues: 1164 helix: 2.38 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 624 TYR 0.021 0.001 TYR A 279 PHE 0.021 0.001 PHE A 536 TRP 0.014 0.001 TRP A 333 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9492) covalent geometry : angle 0.52261 (12840) hydrogen bonds : bond 0.03631 ( 631) hydrogen bonds : angle 4.05797 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 462 TYR cc_start: 0.7630 (m-80) cc_final: 0.7250 (m-80) REVERT: A 626 ARG cc_start: 0.5534 (mmt180) cc_final: 0.5076 (mtt180) REVERT: B 206 MET cc_start: 0.7141 (tpp) cc_final: 0.6626 (tpp) REVERT: B 269 ILE cc_start: 0.6693 (tp) cc_final: 0.6452 (tp) REVERT: B 619 MET cc_start: 0.8040 (ttm) cc_final: 0.7789 (ttm) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.0606 time to fit residues: 12.4200 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 728 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 chunk 105 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 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 = 0.4679 r_free = 0.4679 target = 0.225349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172406 restraints weight = 10236.757| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.64 r_work: 0.3945 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9492 Z= 0.122 Angle : 0.553 15.638 12840 Z= 0.277 Chirality : 0.039 0.204 1400 Planarity : 0.003 0.033 1616 Dihedral : 4.012 26.529 1296 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.64 % Allowed : 17.38 % Favored : 80.98 % 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: 1.84 (0.25), residues: 1164 helix: 2.35 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -1.12 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 624 TYR 0.015 0.001 TYR A 564 PHE 0.023 0.001 PHE A 536 TRP 0.012 0.001 TRP A 300 HIS 0.003 0.001 HIS B 474 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9492) covalent geometry : angle 0.55254 (12840) hydrogen bonds : bond 0.03818 ( 631) hydrogen bonds : angle 4.06849 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.77 seconds wall clock time: 30 minutes 24.43 seconds (1824.43 seconds total)