Starting phenix.real_space_refine on Mon May 12 21:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jli_36398/05_2025/8jli_36398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jli_36398/05_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_36398/05_2025/8jli_36398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jli_36398/05_2025/8jli_36398.map" model { file = "/net/cci-nas-00/data/ceres_data/8jli_36398/05_2025/8jli_36398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jli_36398/05_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-5687/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: 5.98, per 1000 atoms: 0.65 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: 2.20 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: 1.00 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: 2.89 Time building geometry restraints manager: 2.58 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.11820 ( 631) hydrogen bonds : angle 6.24150 ( 1869) covalent geometry : bond 0.00832 ( 9492) covalent geometry : angle 0.99700 (12840) *********************** 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 : 0.911 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: 0.2569 time to fit residues: 75.0772 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 : 0.941 ------------------------------------------------------------------------------- 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 = 0.222723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169762 restraints weight = 10230.136| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.64 r_work: 0.4029 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- 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= 0.152 Angle : 0.563 6.523 12840 Z= 0.303 Chirality : 0.041 0.153 1400 Planarity : 0.004 0.030 1616 Dihedral : 4.649 35.393 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 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 631) hydrogen bonds : angle 4.88212 ( 1869) covalent geometry : bond 0.00331 ( 9492) covalent geometry : angle 0.56319 (12840) *********************** 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 : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7882 (mmm160) REVERT: A 145 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7376 (mtm-85) REVERT: A 367 HIS cc_start: 0.3187 (OUTLIER) cc_final: 0.2506 (t70) REVERT: A 465 THR cc_start: 0.7497 (m) cc_final: 0.7291 (m) REVERT: A 626 ARG cc_start: 0.5355 (mmt180) cc_final: 0.5090 (mtt180) REVERT: B 376 GLN cc_start: 0.7179 (tt0) cc_final: 0.6702 (tp40) REVERT: B 544 THR cc_start: 0.7413 (m) cc_final: 0.7212 (m) REVERT: B 641 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6711 (t80) outliers start: 26 outliers final: 11 residues processed: 161 average time/residue: 0.2209 time to fit residues: 48.9417 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 : 1.050 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 = 0.4629 r_free = 0.4629 target = 0.219173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.165512 restraints weight = 10543.956| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.69 r_work: 0.3900 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9492 Z= 0.170 Angle : 0.573 7.012 12840 Z= 0.305 Chirality : 0.041 0.142 1400 Planarity : 0.004 0.031 1616 Dihedral : 4.693 37.820 1296 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.66 % Allowed : 11.04 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1164 helix: 1.78 (0.18), residues: 768 sheet: 1.25 (1.34), residues: 20 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.004 0.001 HIS B 161 PHE 0.026 0.002 PHE A 245 TYR 0.018 0.002 TYR A 169 ARG 0.006 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 631) hydrogen bonds : angle 4.64454 ( 1869) covalent geometry : bond 0.00389 ( 9492) covalent geometry : angle 0.57313 (12840) *********************** 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 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7456 (mtm-85) REVERT: A 253 GLN cc_start: 0.7271 (mm110) cc_final: 0.6927 (mm-40) REVERT: A 367 HIS cc_start: 0.3679 (OUTLIER) cc_final: 0.2905 (t70) REVERT: A 626 ARG cc_start: 0.5573 (mmt180) cc_final: 0.5205 (mtt180) REVERT: B 201 ASP cc_start: 0.7282 (t0) cc_final: 0.7057 (t0) REVERT: B 346 PHE cc_start: 0.6203 (m-10) cc_final: 0.5993 (t80) REVERT: B 376 GLN cc_start: 0.7430 (tt0) cc_final: 0.6725 (tp40) REVERT: B 451 MET cc_start: 0.7873 (mtm) cc_final: 0.7602 (mtp) REVERT: B 485 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6219 (mtmm) REVERT: B 544 THR cc_start: 0.7496 (m) cc_final: 0.7271 (m) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.2098 time to fit residues: 42.1548 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 : 0.875 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4671 r_free = 0.4671 target = 0.223894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171403 restraints weight = 10303.105| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.75 r_work: 0.3967 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3610 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= 0.135 Angle : 0.521 9.502 12840 Z= 0.275 Chirality : 0.039 0.136 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.511 34.982 1296 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.76 % Allowed : 12.99 % Favored : 84.25 % 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: 1.50 (0.25), residues: 1164 helix: 1.99 (0.18), residues: 768 sheet: 1.13 (1.34), residues: 20 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.004 0.001 HIS B 474 PHE 0.021 0.001 PHE A 245 TYR 0.016 0.001 TYR A 279 ARG 0.003 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 631) hydrogen bonds : angle 4.39560 ( 1869) covalent geometry : bond 0.00298 ( 9492) covalent geometry : angle 0.52055 (12840) *********************** 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 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLN cc_start: 0.7358 (mm110) cc_final: 0.6985 (mm-40) REVERT: A 564 TYR cc_start: 0.6260 (p90) cc_final: 0.5936 (p90) REVERT: A 578 HIS cc_start: 0.6942 (t-90) cc_final: 0.6712 (t-170) REVERT: A 626 ARG cc_start: 0.5442 (mmt180) cc_final: 0.5056 (mtt180) REVERT: A 693 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7299 (t) REVERT: A 742 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6521 (tm-30) REVERT: B 206 MET cc_start: 0.6709 (tpp) cc_final: 0.6473 (tpp) REVERT: B 451 MET cc_start: 0.7782 (mtm) cc_final: 0.7532 (mtp) REVERT: B 471 MET cc_start: 0.7534 (tpp) cc_final: 0.7312 (tpp) REVERT: B 485 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6248 (mtmm) outliers start: 27 outliers final: 20 residues processed: 141 average time/residue: 0.2046 time to fit residues: 41.3980 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 21 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4634 r_free = 0.4634 target = 0.219942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166428 restraints weight = 10409.027| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.78 r_work: 0.3966 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3892 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 : 0.511 11.324 12840 Z= 0.268 Chirality : 0.039 0.141 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.380 34.492 1296 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 13.50 % Favored : 83.33 % 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: 1.62 (0.25), residues: 1164 helix: 2.11 (0.19), residues: 768 sheet: 0.94 (1.33), 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 B 262 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 631) hydrogen bonds : angle 4.27518 ( 1869) covalent geometry : bond 0.00288 ( 9492) covalent geometry : angle 0.51145 (12840) *********************** 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 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5491 (mmt180) cc_final: 0.5070 (mtt180) REVERT: A 651 MET cc_start: 0.6880 (mmt) cc_final: 0.6546 (mmt) REVERT: A 693 CYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7369 (t) REVERT: A 742 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 206 MET cc_start: 0.6839 (tpp) cc_final: 0.6621 (tpp) REVERT: B 451 MET cc_start: 0.7891 (mtm) cc_final: 0.7657 (mtp) REVERT: B 485 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6335 (mtmm) REVERT: B 494 HIS cc_start: 0.6785 (t-90) cc_final: 0.6534 (t-90) outliers start: 31 outliers final: 27 residues processed: 140 average time/residue: 0.1749 time to fit residues: 36.1312 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 367 HIS 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 708 VAL 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: 0.9990 chunk 83 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.219743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166242 restraints weight = 10375.695| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.82 r_work: 0.3961 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4082 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= 0.128 Angle : 0.518 12.792 12840 Z= 0.269 Chirality : 0.039 0.171 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.308 33.446 1296 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.66 % Allowed : 14.83 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.25), residues: 1164 helix: 2.17 (0.19), residues: 768 sheet: 0.70 (1.27), residues: 20 loop : -1.13 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.010 0.001 HIS A 578 PHE 0.020 0.001 PHE A 245 TYR 0.012 0.001 TYR B 306 ARG 0.003 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 631) hydrogen bonds : angle 4.24427 ( 1869) covalent geometry : bond 0.00285 ( 9492) covalent geometry : angle 0.51771 (12840) *********************** 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 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 ARG cc_start: 0.5512 (mmt180) cc_final: 0.5074 (mtt180) REVERT: A 693 CYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7345 (t) REVERT: A 742 GLN cc_start: 0.7003 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 206 MET cc_start: 0.6816 (tpp) cc_final: 0.6614 (tpp) REVERT: B 451 MET cc_start: 0.7871 (mtm) cc_final: 0.7631 (mtp) REVERT: B 485 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6229 (mtmm) REVERT: B 494 HIS cc_start: 0.6886 (t-90) cc_final: 0.6627 (t-90) REVERT: B 693 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.7003 (t) outliers start: 26 outliers final: 21 residues processed: 137 average time/residue: 0.1807 time to fit residues: 36.5356 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 578 HIS 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 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: 0.4980 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 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 = 0.222038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.169029 restraints weight = 10401.417| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.76 r_work: 0.3907 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4229 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= 0.141 Angle : 0.534 14.242 12840 Z= 0.275 Chirality : 0.040 0.181 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.370 34.023 1296 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.97 % Allowed : 15.75 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 766 sheet: 0.67 (1.26), residues: 20 loop : -1.12 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 300 HIS 0.013 0.001 HIS A 578 PHE 0.021 0.001 PHE A 245 TYR 0.014 0.001 TYR B 306 ARG 0.003 0.000 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 631) hydrogen bonds : angle 4.26351 ( 1869) covalent geometry : bond 0.00321 ( 9492) covalent geometry : angle 0.53369 (12840) *********************** 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 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.4990 (OUTLIER) cc_final: 0.4699 (mt) REVERT: A 626 ARG cc_start: 0.5532 (mmt180) cc_final: 0.5120 (mtt180) REVERT: A 651 MET cc_start: 0.6993 (mmt) cc_final: 0.6505 (mmt) REVERT: A 693 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7468 (t) REVERT: B 451 MET cc_start: 0.7891 (mtm) cc_final: 0.7657 (mtp) REVERT: B 485 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6191 (mtmm) REVERT: B 494 HIS cc_start: 0.6972 (t-90) cc_final: 0.6727 (t-90) REVERT: B 693 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6951 (t) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.1718 time to fit residues: 33.8042 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 446 ILE 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 693 CYS Chi-restraints excluded: chain A residue 718 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 367 HIS 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: 7.9990 chunk 93 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 chunk 62 optimal weight: 0.1980 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.223973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171146 restraints weight = 10431.199| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.78 r_work: 0.3972 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.4381 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= 0.119 Angle : 0.512 15.099 12840 Z= 0.262 Chirality : 0.039 0.212 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.201 31.651 1296 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.45 % Allowed : 16.05 % Favored : 81.49 % 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: 1.75 (0.25), residues: 1164 helix: 2.23 (0.19), residues: 768 sheet: 0.59 (1.24), residues: 20 loop : -1.16 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 300 HIS 0.004 0.001 HIS B 474 PHE 0.018 0.001 PHE A 245 TYR 0.014 0.001 TYR A 564 ARG 0.002 0.000 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 631) hydrogen bonds : angle 4.16133 ( 1869) covalent geometry : bond 0.00259 ( 9492) covalent geometry : angle 0.51173 (12840) *********************** 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 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 446 ILE cc_start: 0.4951 (OUTLIER) cc_final: 0.4622 (mt) REVERT: A 626 ARG cc_start: 0.5507 (mmt180) cc_final: 0.5073 (mtt180) REVERT: A 651 MET cc_start: 0.6826 (mmt) cc_final: 0.6402 (mmt) REVERT: B 206 MET cc_start: 0.7036 (tpp) cc_final: 0.6545 (tpp) REVERT: B 451 MET cc_start: 0.7821 (mtm) cc_final: 0.7579 (mtp) REVERT: B 471 MET cc_start: 0.7679 (tpp) cc_final: 0.6937 (tpt) REVERT: B 485 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6374 (mtmm) REVERT: B 494 HIS cc_start: 0.7117 (t-90) cc_final: 0.6903 (t-90) REVERT: B 619 MET cc_start: 0.8070 (ttm) cc_final: 0.7803 (ttm) REVERT: B 693 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6978 (t) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.1752 time to fit residues: 33.8807 Evaluate side-chains 130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 446 ILE 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 485 LYS 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: 0.8980 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 104 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.219625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168409 restraints weight = 10363.346| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.38 r_work: 0.3974 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4483 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= 0.129 Angle : 0.547 16.140 12840 Z= 0.278 Chirality : 0.039 0.203 1400 Planarity : 0.003 0.031 1616 Dihedral : 4.269 31.928 1296 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.04 % Allowed : 16.77 % Favored : 81.19 % 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: 1.68 (0.25), residues: 1164 helix: 2.17 (0.19), residues: 768 sheet: 0.59 (1.22), residues: 20 loop : -1.17 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 300 HIS 0.004 0.001 HIS B 474 PHE 0.021 0.001 PHE A 245 TYR 0.018 0.001 TYR B 306 ARG 0.002 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 631) hydrogen bonds : angle 4.19897 ( 1869) covalent geometry : bond 0.00290 ( 9492) covalent geometry : angle 0.54698 (12840) *********************** 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 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 446 ILE cc_start: 0.5186 (OUTLIER) cc_final: 0.4828 (mt) REVERT: A 626 ARG cc_start: 0.5696 (mmt180) cc_final: 0.5151 (mtt180) REVERT: A 651 MET cc_start: 0.6796 (mmt) cc_final: 0.6444 (mmt) REVERT: B 206 MET cc_start: 0.7214 (tpp) cc_final: 0.6742 (tpp) REVERT: B 269 ILE cc_start: 0.6825 (tp) cc_final: 0.6586 (tp) REVERT: B 451 MET cc_start: 0.7970 (mtm) cc_final: 0.7756 (mtp) REVERT: B 471 MET cc_start: 0.7969 (tpp) cc_final: 0.7186 (tpt) REVERT: B 485 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6419 (mtmm) REVERT: B 494 HIS cc_start: 0.7233 (t-90) cc_final: 0.7030 (t-90) REVERT: B 619 MET cc_start: 0.8234 (ttm) cc_final: 0.7992 (ttm) REVERT: B 693 CYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7021 (t) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.1806 time to fit residues: 35.1806 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 446 ILE 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 485 LYS 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: 0.6980 chunk 21 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.4688 r_free = 0.4688 target = 0.226580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174620 restraints weight = 10298.678| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.56 r_work: 0.4002 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4652 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= 0.116 Angle : 0.531 16.564 12840 Z= 0.267 Chirality : 0.039 0.205 1400 Planarity : 0.003 0.033 1616 Dihedral : 4.134 28.898 1296 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.25 % Allowed : 17.38 % Favored : 80.37 % 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: 1.80 (0.25), residues: 1164 helix: 2.33 (0.19), residues: 758 sheet: 0.75 (1.19), residues: 20 loop : -1.19 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 300 HIS 0.005 0.001 HIS B 474 PHE 0.020 0.001 PHE A 536 TYR 0.021 0.001 TYR A 279 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 631) hydrogen bonds : angle 4.11836 ( 1869) covalent geometry : bond 0.00251 ( 9492) covalent geometry : angle 0.53131 (12840) ********************** 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 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 446 ILE cc_start: 0.4944 (OUTLIER) cc_final: 0.4611 (mt) REVERT: A 462 TYR cc_start: 0.7612 (m-80) cc_final: 0.7210 (m-80) REVERT: A 626 ARG cc_start: 0.5529 (mmt180) cc_final: 0.5095 (mtt180) REVERT: A 651 MET cc_start: 0.6874 (mmt) cc_final: 0.6552 (mmt) REVERT: B 206 MET cc_start: 0.7145 (tpp) cc_final: 0.6692 (tpp) REVERT: B 269 ILE cc_start: 0.6608 (tp) cc_final: 0.6361 (tp) REVERT: B 310 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6333 (ttt) REVERT: B 471 MET cc_start: 0.7687 (tpp) cc_final: 0.6991 (tpt) REVERT: B 485 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6429 (mtmm) REVERT: B 619 MET cc_start: 0.8106 (ttm) cc_final: 0.7852 (ttm) REVERT: B 693 CYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6999 (t) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.1876 time to fit residues: 38.0890 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 446 ILE 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 310 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 485 LYS 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 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4630 r_free = 0.4630 target = 0.219873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165466 restraints weight = 10329.502| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.85 r_work: 0.3890 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4744 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= 0.141 Angle : 0.562 16.365 12840 Z= 0.283 Chirality : 0.040 0.206 1400 Planarity : 0.003 0.030 1616 Dihedral : 4.314 31.405 1296 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.25 % Allowed : 17.89 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1164 helix: 2.19 (0.19), residues: 760 sheet: 0.97 (1.21), residues: 20 loop : -1.25 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 300 HIS 0.005 0.001 HIS B 161 PHE 0.023 0.001 PHE A 536 TYR 0.015 0.001 TYR B 306 ARG 0.002 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 631) hydrogen bonds : angle 4.17581 ( 1869) covalent geometry : bond 0.00321 ( 9492) covalent geometry : angle 0.56209 (12840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.89 seconds wall clock time: 76 minutes 54.64 seconds (4614.64 seconds total)