Starting phenix.real_space_refine on Thu Mar 13 23:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jli_36398/03_2025/8jli_36398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jli_36398/03_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_36398/03_2025/8jli_36398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jli_36398/03_2025/8jli_36398.map" model { file = "/net/cci-nas-00/data/ceres_data/8jli_36398/03_2025/8jli_36398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jli_36398/03_2025/8jli_36398.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.24, per 1000 atoms: 0.67 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 2.75 Time building geometry restraints manager: 2.68 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: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- 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= 0.548 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.038 0.009 TRP B 166 HIS 0.018 0.003 HIS B 161 PHE 0.066 0.006 PHE A 644 TYR 0.043 0.006 TYR A 212 ARG 0.040 0.003 ARG A 624 *********************** 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 : 0.946 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: 0.3175 time to fit residues: 92.9657 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 : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.222724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169764 restraints weight = 10230.014| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.64 r_work: 0.4031 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9492 Z= 0.213 Angle : 0.563 6.523 12840 Z= 0.303 Chirality : 0.041 0.153 1400 Planarity : 0.004 0.030 1616 Dihedral : 4.649 35.394 1296 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.66 % Allowed : 7.16 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1164 helix: 1.81 (0.18), residues: 764 sheet: -0.14 (0.42), residues: 160 loop : -1.43 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.006 0.001 HIS B 387 PHE 0.021 0.002 PHE A 245 TYR 0.023 0.002 TYR B 462 ARG 0.005 0.001 ARG B 142 *********************** 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 170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7878 (mmm160) REVERT: A 145 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7377 (mtm-85) REVERT: A 367 HIS cc_start: 0.3189 (OUTLIER) cc_final: 0.2507 (t70) REVERT: A 465 THR cc_start: 0.7498 (m) cc_final: 0.7294 (m) REVERT: A 626 ARG cc_start: 0.5354 (mmt180) cc_final: 0.5088 (mtt180) REVERT: B 376 GLN cc_start: 0.7183 (tt0) cc_final: 0.6708 (tp40) REVERT: B 641 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6720 (t80) outliers start: 26 outliers final: 11 residues processed: 161 average time/residue: 0.2320 time to fit residues: 51.5520 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4635 r_free = 0.4635 target = 0.219935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.166349 restraints weight = 10522.239| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.73 r_work: 0.3898 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9492 Z= 0.249 Angle : 0.566 7.258 12840 Z= 0.302 Chirality : 0.041 0.137 1400 Planarity : 0.004 0.029 1616 Dihedral : 4.657 37.467 1296 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.66 % Allowed : 10.94 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1164 helix: 1.80 (0.18), residues: 768 sheet: 1.26 (1.34), residues: 20 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 371 HIS 0.004 0.001 HIS B 161 PHE 0.025 0.002 PHE A 245 TYR 0.017 0.002 TYR A 169 ARG 0.009 0.001 ARG B 228 *********************** 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 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7437 (mtm-85) REVERT: A 253 GLN cc_start: 0.7288 (mm110) cc_final: 0.6951 (mm-40) REVERT: A 367 HIS cc_start: 0.3701 (OUTLIER) cc_final: 0.2917 (t70) REVERT: A 626 ARG cc_start: 0.5562 (mmt180) cc_final: 0.5185 (mtt180) REVERT: B 201 ASP cc_start: 0.7259 (t0) cc_final: 0.7032 (t0) REVERT: B 346 PHE cc_start: 0.6210 (m-10) cc_final: 0.5982 (t80) REVERT: B 376 GLN cc_start: 0.7447 (tt0) cc_final: 0.7043 (tp40) REVERT: B 451 MET cc_start: 0.7879 (mtm) cc_final: 0.7615 (mtp) REVERT: B 485 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6283 (mtmm) REVERT: B 651 MET cc_start: 0.6729 (tpp) cc_final: 0.6348 (tpp) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 0.2074 time to fit residues: 42.0935 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 367 HIS 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 642 LEU Chi-restraints excluded: chain A residue 718 PHE 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 485 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 631 SER 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 69 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4668 r_free = 0.4668 target = 0.223762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171387 restraints weight = 10299.043| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.74 r_work: 0.3964 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3593 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= 0.197 Angle : 0.524 9.030 12840 Z= 0.277 Chirality : 0.039 0.138 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.519 35.071 1296 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.66 % Allowed : 12.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1164 helix: 1.96 (0.18), residues: 768 sheet: 1.11 (1.35), residues: 20 loop : -1.18 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 432 HIS 0.004 0.001 HIS A 578 PHE 0.021 0.001 PHE A 686 TYR 0.017 0.001 TYR A 279 ARG 0.004 0.000 ARG A 141 *********************** 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 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7418 (mtm-85) REVERT: A 253 GLN cc_start: 0.7321 (mm110) cc_final: 0.6966 (mm-40) REVERT: A 564 TYR cc_start: 0.6269 (p90) cc_final: 0.5970 (p90) REVERT: A 578 HIS cc_start: 0.6899 (t-90) cc_final: 0.6673 (t-170) REVERT: A 626 ARG cc_start: 0.5464 (mmt180) cc_final: 0.5065 (mtt180) REVERT: A 693 CYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7479 (t) REVERT: B 206 MET cc_start: 0.6695 (tpp) cc_final: 0.6459 (tpp) REVERT: B 346 PHE cc_start: 0.6262 (m-10) cc_final: 0.6051 (t80) REVERT: B 451 MET cc_start: 0.7791 (mtm) cc_final: 0.7532 (mtp) REVERT: B 471 MET cc_start: 0.7465 (tpp) cc_final: 0.7262 (tpp) REVERT: B 485 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6276 (mtmm) REVERT: B 651 MET cc_start: 0.6701 (tpp) cc_final: 0.6347 (tpp) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 0.3584 time to fit residues: 73.8774 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 614 VAL Chi-restraints excluded: chain A residue 634 MET 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 485 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4643 r_free = 0.4643 target = 0.220916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.167492 restraints weight = 10434.768| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.72 r_work: 0.3932 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3838 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= 0.175 Angle : 0.506 10.709 12840 Z= 0.266 Chirality : 0.039 0.133 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.372 34.364 1296 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.97 % Allowed : 13.60 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1164 helix: 2.13 (0.19), residues: 768 sheet: 1.03 (1.35), residues: 20 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS B 474 PHE 0.020 0.001 PHE A 245 TYR 0.017 0.001 TYR A 279 ARG 0.003 0.000 ARG A 141 *********************** 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 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLN cc_start: 0.7285 (mm110) cc_final: 0.6926 (mm-40) REVERT: A 578 HIS cc_start: 0.6927 (t-90) cc_final: 0.6720 (t-170) REVERT: A 626 ARG cc_start: 0.5533 (mmt180) cc_final: 0.5170 (mtt180) REVERT: A 651 MET cc_start: 0.6891 (mmt) cc_final: 0.6510 (mmt) REVERT: A 693 CYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7407 (t) REVERT: A 742 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6514 (tm-30) REVERT: B 206 MET cc_start: 0.6830 (tpp) cc_final: 0.6612 (tpp) REVERT: B 451 MET cc_start: 0.7861 (mtm) cc_final: 0.7610 (mtp) REVERT: B 485 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6328 (mtmm) outliers start: 29 outliers final: 24 residues processed: 140 average time/residue: 0.2208 time to fit residues: 44.9740 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 614 VAL Chi-restraints excluded: chain A residue 634 MET 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 202 SER 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 485 LYS 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 7 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.218223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164223 restraints weight = 10426.895| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.82 r_work: 0.3896 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4105 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= 0.210 Angle : 0.536 12.405 12840 Z= 0.280 Chirality : 0.040 0.176 1400 Planarity : 0.003 0.035 1616 Dihedral : 4.477 35.394 1296 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 14.31 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1164 helix: 2.05 (0.18), residues: 768 sheet: 0.74 (1.28), residues: 20 loop : -1.17 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.005 0.001 HIS B 474 PHE 0.022 0.001 PHE A 245 TYR 0.015 0.001 TYR B 306 ARG 0.009 0.000 ARG B 483 *********************** 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 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5560 (mmt180) cc_final: 0.5144 (mtt180) REVERT: A 693 CYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7492 (t) REVERT: A 742 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 206 MET cc_start: 0.6948 (tpp) cc_final: 0.6738 (tpp) REVERT: B 451 MET cc_start: 0.7899 (mtm) cc_final: 0.7665 (mtp) REVERT: B 485 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6184 (mtmm) REVERT: B 693 CYS cc_start: 0.7288 (OUTLIER) cc_final: 0.7049 (t) outliers start: 26 outliers final: 22 residues processed: 132 average time/residue: 0.1848 time to fit residues: 36.0788 Evaluate side-chains 135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 614 VAL Chi-restraints excluded: chain A residue 634 MET 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 202 SER 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 485 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 693 CYS 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 17 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 578 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.215917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.161558 restraints weight = 10589.163| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.87 r_work: 0.3912 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9492 Z= 0.235 Angle : 0.558 14.039 12840 Z= 0.292 Chirality : 0.040 0.191 1400 Planarity : 0.004 0.031 1616 Dihedral : 4.645 36.354 1296 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.07 % Allowed : 15.54 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1164 helix: 1.97 (0.19), residues: 768 sheet: 0.68 (1.25), residues: 20 loop : -1.23 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.011 0.001 HIS A 578 PHE 0.021 0.002 PHE A 245 TYR 0.016 0.001 TYR B 306 ARG 0.003 0.000 ARG B 262 *********************** 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 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5503 (mmt180) cc_final: 0.5048 (mtt180) REVERT: A 651 MET cc_start: 0.6964 (mmt) cc_final: 0.6484 (mmt) REVERT: A 742 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 451 MET cc_start: 0.7941 (mtm) cc_final: 0.7729 (mtp) REVERT: B 485 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6230 (mtmm) REVERT: B 619 MET cc_start: 0.8150 (ttm) cc_final: 0.7897 (ttm) REVERT: B 693 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6865 (t) outliers start: 30 outliers final: 24 residues processed: 132 average time/residue: 0.1875 time to fit residues: 36.5791 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 578 HIS 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 642 LEU Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain B residue 156 LEU 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 485 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 693 CYS 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 40 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 494 HIS A 578 HIS B 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.216688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.164935 restraints weight = 10620.889| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.51 r_work: 0.3903 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4436 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= 0.200 Angle : 0.551 15.053 12840 Z= 0.282 Chirality : 0.039 0.191 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.568 35.582 1296 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 16.46 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1164 helix: 2.05 (0.19), residues: 768 sheet: 0.63 (1.23), residues: 20 loop : -1.23 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.023 0.001 HIS A 578 PHE 0.020 0.001 PHE A 245 TYR 0.013 0.001 TYR A 564 ARG 0.002 0.000 ARG B 624 *********************** 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 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 462 TYR cc_start: 0.7535 (m-80) cc_final: 0.7144 (m-80) REVERT: A 626 ARG cc_start: 0.5521 (mmt180) cc_final: 0.5107 (mtt180) REVERT: A 651 MET cc_start: 0.6981 (mmt) cc_final: 0.6519 (mmt) REVERT: A 742 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 206 MET cc_start: 0.7247 (tpp) cc_final: 0.6722 (tpp) REVERT: B 451 MET cc_start: 0.7897 (mtm) cc_final: 0.7669 (mtp) REVERT: B 485 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6304 (mtmm) REVERT: B 619 MET cc_start: 0.8130 (ttm) cc_final: 0.7880 (ttm) REVERT: B 693 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6966 (t) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.1829 time to fit residues: 35.7748 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 634 MET 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 367 HIS Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 693 CYS 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 4 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 104 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.218044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166917 restraints weight = 10433.006| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.46 r_work: 0.3925 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9492 Z= 0.187 Angle : 0.546 15.883 12840 Z= 0.276 Chirality : 0.039 0.217 1400 Planarity : 0.003 0.032 1616 Dihedral : 4.428 34.116 1296 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 16.97 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1164 helix: 2.11 (0.19), residues: 770 sheet: 0.84 (1.20), residues: 20 loop : -1.22 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.005 0.001 HIS B 474 PHE 0.019 0.001 PHE A 245 TYR 0.021 0.001 TYR A 279 ARG 0.002 0.000 ARG B 624 *********************** 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 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 462 TYR cc_start: 0.7484 (m-80) cc_final: 0.7083 (m-80) REVERT: A 626 ARG cc_start: 0.5496 (mmt180) cc_final: 0.5060 (mtt180) REVERT: A 651 MET cc_start: 0.6882 (mmt) cc_final: 0.6402 (mmt) REVERT: B 206 MET cc_start: 0.7273 (tpp) cc_final: 0.6788 (tpp) REVERT: B 451 MET cc_start: 0.7861 (mtm) cc_final: 0.7621 (mtp) REVERT: B 485 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6307 (mtmm) REVERT: B 619 MET cc_start: 0.8153 (ttm) cc_final: 0.7913 (ttm) REVERT: B 693 CYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6952 (t) outliers start: 24 outliers final: 20 residues processed: 134 average time/residue: 0.1808 time to fit residues: 35.6330 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 634 MET 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 367 HIS Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 693 CYS 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 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 94 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.222136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.171085 restraints weight = 10603.962| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.52 r_work: 0.4011 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9492 Z= 0.146 Angle : 0.518 16.198 12840 Z= 0.259 Chirality : 0.038 0.205 1400 Planarity : 0.003 0.033 1616 Dihedral : 4.073 28.547 1296 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.53 % Allowed : 18.00 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1164 helix: 2.39 (0.19), residues: 760 sheet: 0.94 (1.19), residues: 20 loop : -1.17 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 300 HIS 0.005 0.001 HIS B 474 PHE 0.022 0.001 PHE A 536 TYR 0.015 0.001 TYR A 564 ARG 0.002 0.000 ARG B 483 ********************** 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 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5498 (mmm) REVERT: A 462 TYR cc_start: 0.7608 (m-80) cc_final: 0.7223 (m-80) REVERT: A 626 ARG cc_start: 0.5479 (mmt180) cc_final: 0.5029 (mtt180) REVERT: A 651 MET cc_start: 0.6746 (mmt) cc_final: 0.6455 (mmt) REVERT: B 471 MET cc_start: 0.7538 (tpp) cc_final: 0.6885 (tpt) REVERT: B 485 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6447 (mtmm) REVERT: B 619 MET cc_start: 0.7999 (ttm) cc_final: 0.7704 (ttm) outliers start: 15 outliers final: 12 residues processed: 134 average time/residue: 0.1824 time to fit residues: 36.0992 Evaluate side-chains 128 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 586 ASP 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 353 THR Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.218978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167368 restraints weight = 10470.164| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.48 r_work: 0.3927 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4801 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= 0.187 Angle : 0.543 16.000 12840 Z= 0.273 Chirality : 0.039 0.202 1400 Planarity : 0.003 0.032 1616 Dihedral : 4.181 30.161 1296 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.84 % Allowed : 17.48 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1164 helix: 2.31 (0.19), residues: 758 sheet: 1.16 (1.22), residues: 20 loop : -1.25 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 300 HIS 0.004 0.001 HIS B 474 PHE 0.022 0.001 PHE A 536 TYR 0.021 0.001 TYR A 279 ARG 0.002 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.41 seconds wall clock time: 83 minutes 4.05 seconds (4984.05 seconds total)