Starting phenix.real_space_refine on Tue Nov 18 06:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6t_44277/11_2025/9b6t_44277.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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 45 5.16 5 C 7628 2.51 5 N 2113 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12108 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 193} Chain breaks: 7 Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain breaks: 1 Chain: "C" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2835 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 329} Chain breaks: 5 Chain: "D" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 193} Chain breaks: 7 Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 706 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2835 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 329} Chain breaks: 5 Chain: "H" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12108 At special positions: 0 Unit cell: (142.628, 103.532, 95.568, 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 45 16.00 O 2322 8.00 N 2113 7.00 C 7628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 619.1 milliseconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 38 sheets defined 8.8% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.729A pdb=" N ALA A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.647A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.972A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.664A pdb=" N SER C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.932A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 563 through 569 removed outlier: 4.282A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 4.176A pdb=" N ASN D 254 " --> pdb=" O THR D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 355 through 359 removed outlier: 3.624A pdb=" N SER D 358 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 359 " --> pdb=" O LEU D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 359' Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'E' and resid 431 through 435 removed outlier: 4.057A pdb=" N LEU E 435 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.889A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.950A pdb=" N ALA F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 563 through 569 removed outlier: 4.361A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'L' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 261 removed outlier: 3.852A pdb=" N GLN A 646 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 removed outlier: 7.665A pdb=" N THR A 279 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR A 379 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP A 281 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 629 removed outlier: 4.036A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.961A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.874A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB1, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.067A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 231 through 235 removed outlier: 9.575A pdb=" N PHE C 372 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 246 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 231 through 235 removed outlier: 6.982A pdb=" N GLU C 684 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 686 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 308 " --> pdb=" O GLU C 686 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN C 688 " --> pdb=" O TRP C 306 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 308 " --> pdb=" O HIS C 423 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.281A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.659A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AB7, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AB8, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AB9, first strand: chain 'D' and resid 258 through 261 removed outlier: 4.064A pdb=" N GLN D 646 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 258 through 261 removed outlier: 7.553A pdb=" N THR D 279 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR D 379 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP D 281 " --> pdb=" O TYR D 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.068A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 578 through 581 removed outlier: 4.118A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 627 through 629 removed outlier: 4.008A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.562A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AC7, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.218A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 231 through 235 removed outlier: 9.422A pdb=" N PHE F 372 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR F 246 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.560A pdb=" N GLY F 307 " --> pdb=" O GLN F 688 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE F 308 " --> pdb=" O HIS F 423 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 426 through 428 Processing sheet with id=AD2, first strand: chain 'F' and resid 445 through 451 removed outlier: 6.525A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AD4, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AD5, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.618A pdb=" N GLN H 24 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 30 through 31 removed outlier: 5.201A pdb=" N TYR H 52 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP H 53 " --> pdb=" O HIS H 69 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS H 69 " --> pdb=" O TRP H 53 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.739A pdb=" N CYS H 114 " --> pdb=" O TRP H 129 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP H 129 " --> pdb=" O CYS H 114 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG H 116 " --> pdb=" O ASP H 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.211A pdb=" N GLN L 58 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU L 67 " --> pdb=" O GLN L 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AE2, first strand: chain 'L' and resid 38 through 43 279 hydrogen bonds defined for protein. 597 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: 2.07 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3857 1.33 - 1.45: 2022 1.45 - 1.57: 6480 1.57 - 1.69: 0 1.69 - 1.80: 78 Bond restraints: 12437 Sorted by residual: bond pdb=" C HIS F 630 " pdb=" N PRO F 631 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.08e-02 8.57e+03 6.54e+00 bond pdb=" C HIS C 630 " pdb=" N PRO C 631 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.08e-02 8.57e+03 5.22e+00 bond pdb=" C HIS D 630 " pdb=" N PRO D 631 " ideal model delta sigma weight residual 1.336 1.311 0.024 1.08e-02 8.57e+03 5.11e+00 bond pdb=" CB PHE H 97 " pdb=" CG PHE H 97 " ideal model delta sigma weight residual 1.502 1.452 0.050 2.30e-02 1.89e+03 4.78e+00 bond pdb=" C PRO C 365 " pdb=" O PRO C 365 " ideal model delta sigma weight residual 1.246 1.227 0.018 8.50e-03 1.38e+04 4.73e+00 ... (remaining 12432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 16010 1.90 - 3.79: 779 3.79 - 5.69: 85 5.69 - 7.59: 28 7.59 - 9.48: 9 Bond angle restraints: 16911 Sorted by residual: angle pdb=" C ARG L 75 " pdb=" N PRO L 76 " pdb=" CA PRO L 76 " ideal model delta sigma weight residual 120.03 127.88 -7.85 9.90e-01 1.02e+00 6.29e+01 angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 112.73 121.47 -8.74 1.20e+00 6.94e-01 5.30e+01 angle pdb=" N GLY D 539 " pdb=" CA GLY D 539 " pdb=" C GLY D 539 " ideal model delta sigma weight residual 112.73 121.41 -8.68 1.20e+00 6.94e-01 5.24e+01 angle pdb=" C GLU C 723 " pdb=" N PRO C 724 " pdb=" CA PRO C 724 " ideal model delta sigma weight residual 119.05 127.07 -8.02 1.11e+00 8.12e-01 5.22e+01 angle pdb=" N SER B 448 " pdb=" CA SER B 448 " pdb=" C SER B 448 " ideal model delta sigma weight residual 111.28 118.30 -7.02 1.09e+00 8.42e-01 4.15e+01 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 6987 16.98 - 33.96: 219 33.96 - 50.94: 55 50.94 - 67.92: 11 67.92 - 84.90: 9 Dihedral angle restraints: 7281 sinusoidal: 2870 harmonic: 4411 Sorted by residual: dihedral pdb=" CA LEU D 256 " pdb=" C LEU D 256 " pdb=" N TYR D 257 " pdb=" CA TYR D 257 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA THR C 491 " pdb=" C THR C 491 " pdb=" N THR C 492 " pdb=" CA THR C 492 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLU C 698 " pdb=" C GLU C 698 " pdb=" N ILE C 699 " pdb=" CA ILE C 699 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1434 0.074 - 0.148: 290 0.148 - 0.222: 29 0.222 - 0.295: 3 0.295 - 0.369: 1 Chirality restraints: 1757 Sorted by residual: chirality pdb=" CA ASN L 72 " pdb=" N ASN L 72 " pdb=" C ASN L 72 " pdb=" CB ASN L 72 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ARG H 124 " pdb=" N ARG H 124 " pdb=" C ARG H 124 " pdb=" CB ARG H 124 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ARG F 730 " pdb=" N ARG F 730 " pdb=" C ARG F 730 " pdb=" CB ARG F 730 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1754 not shown) Planarity restraints: 2227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 655 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PRO D 655 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO D 655 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA D 656 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 493 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C VAL D 493 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL D 493 " -0.020 2.00e-02 2.50e+03 pdb=" N THR D 494 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 64 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO L 65 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " 0.036 5.00e-02 4.00e+02 ... (remaining 2224 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 52 2.46 - 3.07: 8552 3.07 - 3.68: 18243 3.68 - 4.29: 27952 4.29 - 4.90: 46657 Nonbonded interactions: 101456 Sorted by model distance: nonbonded pdb=" OE1 GLU D 500 " pdb=" OG1 THR F 450 " model vdw 1.846 3.040 nonbonded pdb=" OE1 GLN D 486 " pdb=" OG SER D 538 " model vdw 1.959 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" O PRO A 643 " model vdw 2.069 3.040 nonbonded pdb=" O LYS C 545 " pdb=" OG1 THR C 548 " model vdw 2.092 3.040 nonbonded pdb=" NH2 ARG D 485 " pdb=" OG SER D 576 " model vdw 2.145 3.120 ... (remaining 101451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 0.510 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 12439 Z= 0.435 Angle : 0.943 9.482 16915 Z= 0.589 Chirality : 0.057 0.369 1757 Planarity : 0.005 0.065 2227 Dihedral : 10.143 84.903 4463 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.84 % Allowed : 2.36 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 1482 helix: -3.26 (0.47), residues: 62 sheet: -0.75 (0.27), residues: 275 loop : -0.94 (0.15), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 485 TYR 0.031 0.003 TYR H 71 PHE 0.031 0.002 PHE H 97 TRP 0.026 0.003 TRP A 281 HIS 0.009 0.002 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00933 (12437) covalent geometry : angle 0.94301 (16911) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.40871 ( 4) hydrogen bonds : bond 0.22323 ( 249) hydrogen bonds : angle 9.26031 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 0.487 Fit side-chains REVERT: A 488 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.5944 (mmt180) REVERT: A 640 MET cc_start: 0.8393 (mtp) cc_final: 0.8143 (mtp) REVERT: B 601 ILE cc_start: 0.8716 (mm) cc_final: 0.8460 (pt) REVERT: C 514 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8139 (mmt180) REVERT: D 488 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.6605 (mmt180) REVERT: D 640 MET cc_start: 0.7740 (mtp) cc_final: 0.7425 (mtm) REVERT: E 433 ASP cc_start: 0.8829 (p0) cc_final: 0.8572 (p0) REVERT: E 574 THR cc_start: 0.7969 (p) cc_final: 0.7412 (p) REVERT: E 575 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7986 (mm-30) REVERT: F 452 ASN cc_start: 0.8690 (m110) cc_final: 0.8434 (m110) REVERT: H 25 GLU cc_start: 0.8410 (mp0) cc_final: 0.7229 (mp0) REVERT: L 104 GLU cc_start: 0.8894 (tt0) cc_final: 0.8668 (tp30) outliers start: 11 outliers final: 3 residues processed: 267 average time/residue: 0.5247 time to fit residues: 153.4954 Evaluate side-chains 183 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 624 HIS A 646 GLN B 456 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 495 GLN C 585 GLN C 608 GLN C 704 ASN D 624 HIS D 646 GLN E 452 ASN E 585 GLN F 430 GLN F 546 GLN F 608 GLN F 700 GLN H 24 GLN L 117 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065286 restraints weight = 34400.637| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.91 r_work: 0.2987 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12439 Z= 0.177 Angle : 0.615 6.598 16915 Z= 0.324 Chirality : 0.044 0.160 1757 Planarity : 0.004 0.039 2227 Dihedral : 5.261 36.884 1663 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.13 % Allowed : 9.74 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1482 helix: -2.75 (0.53), residues: 72 sheet: -0.30 (0.29), residues: 257 loop : -0.55 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 485 TYR 0.025 0.002 TYR H 71 PHE 0.017 0.002 PHE L 70 TRP 0.011 0.001 TRP C 509 HIS 0.008 0.002 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00401 (12437) covalent geometry : angle 0.61498 (16911) SS BOND : bond 0.00596 ( 2) SS BOND : angle 1.04561 ( 4) hydrogen bonds : bond 0.03649 ( 249) hydrogen bonds : angle 6.21298 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.5763 (mmt180) REVERT: A 595 TRP cc_start: 0.8519 (m100) cc_final: 0.8238 (m100) REVERT: A 626 ASP cc_start: 0.8545 (m-30) cc_final: 0.8207 (m-30) REVERT: B 483 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 601 ILE cc_start: 0.8610 (mm) cc_final: 0.8349 (pt) REVERT: C 471 MET cc_start: 0.8990 (mtm) cc_final: 0.8780 (ttm) REVERT: C 514 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7862 (tmt-80) REVERT: C 516 SER cc_start: 0.8464 (m) cc_final: 0.8074 (p) REVERT: D 361 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8141 (pp20) REVERT: D 488 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.6854 (mmt180) REVERT: D 516 SER cc_start: 0.9483 (m) cc_final: 0.9058 (p) REVERT: D 640 MET cc_start: 0.7905 (mtp) cc_final: 0.7452 (mtm) REVERT: E 574 THR cc_start: 0.7996 (p) cc_final: 0.7607 (p) REVERT: E 575 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8136 (mm-30) REVERT: F 452 ASN cc_start: 0.8728 (m110) cc_final: 0.8226 (m110) REVERT: F 584 HIS cc_start: 0.8793 (m170) cc_final: 0.7979 (t70) REVERT: L 82 ARG cc_start: 0.8749 (ptt-90) cc_final: 0.8541 (ptt90) outliers start: 28 outliers final: 11 residues processed: 233 average time/residue: 0.4763 time to fit residues: 122.5476 Evaluate side-chains 197 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 651 ASN B 477 ASN C 585 GLN E 585 GLN F 599 GLN H 24 GLN ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064676 restraints weight = 34478.531| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.94 r_work: 0.2973 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12439 Z= 0.183 Angle : 0.589 9.599 16915 Z= 0.302 Chirality : 0.043 0.230 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.962 32.772 1660 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.36 % Allowed : 10.96 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1482 helix: -2.50 (0.56), residues: 72 sheet: 0.23 (0.30), residues: 237 loop : -0.42 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 124 TYR 0.020 0.001 TYR H 71 PHE 0.012 0.001 PHE L 70 TRP 0.013 0.001 TRP A 509 HIS 0.005 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00420 (12437) covalent geometry : angle 0.58851 (16911) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.03516 ( 4) hydrogen bonds : bond 0.03132 ( 249) hydrogen bonds : angle 5.70113 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.5783 (mmt180) REVERT: A 595 TRP cc_start: 0.8483 (m100) cc_final: 0.8244 (m100) REVERT: A 601 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7224 (mp) REVERT: A 626 ASP cc_start: 0.8554 (m-30) cc_final: 0.8261 (m-30) REVERT: B 601 ILE cc_start: 0.8576 (mm) cc_final: 0.8089 (pt) REVERT: C 514 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7728 (tmt-80) REVERT: C 516 SER cc_start: 0.8532 (m) cc_final: 0.8097 (p) REVERT: C 592 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: D 361 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8196 (pp20) REVERT: D 488 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.6834 (mmt180) REVERT: D 516 SER cc_start: 0.9492 (m) cc_final: 0.9058 (p) REVERT: D 640 MET cc_start: 0.7929 (mtp) cc_final: 0.7466 (mtm) REVERT: D 664 LYS cc_start: 0.9284 (ttpp) cc_final: 0.9083 (ttpp) REVERT: E 575 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8054 (mm-30) REVERT: F 452 ASN cc_start: 0.8647 (m110) cc_final: 0.8212 (m110) REVERT: F 584 HIS cc_start: 0.8774 (m170) cc_final: 0.7998 (t70) REVERT: F 682 GLU cc_start: 0.4135 (pm20) cc_final: 0.3885 (pm20) REVERT: L 81 ASP cc_start: 0.8750 (t0) cc_final: 0.8533 (t0) REVERT: L 82 ARG cc_start: 0.8791 (ptt-90) cc_final: 0.8435 (ptt90) REVERT: L 126 GLU cc_start: 0.8969 (mp0) cc_final: 0.8529 (mp0) outliers start: 31 outliers final: 16 residues processed: 207 average time/residue: 0.4877 time to fit residues: 111.4332 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 92 optimal weight: 0.0980 chunk 110 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 495 GLN C 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064831 restraints weight = 34285.480| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.91 r_work: 0.2976 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12439 Z= 0.171 Angle : 0.565 9.298 16915 Z= 0.290 Chirality : 0.043 0.234 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.754 32.966 1660 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.04 % Allowed : 11.42 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1482 helix: -2.39 (0.58), residues: 72 sheet: 0.35 (0.30), residues: 237 loop : -0.35 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 485 TYR 0.017 0.001 TYR H 71 PHE 0.013 0.001 PHE L 70 TRP 0.012 0.001 TRP F 509 HIS 0.006 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00394 (12437) covalent geometry : angle 0.56452 (16911) SS BOND : bond 0.00317 ( 2) SS BOND : angle 1.04881 ( 4) hydrogen bonds : bond 0.02846 ( 249) hydrogen bonds : angle 5.40786 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.5808 (mmt180) REVERT: A 601 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7119 (mp) REVERT: A 626 ASP cc_start: 0.8527 (m-30) cc_final: 0.8195 (m-30) REVERT: A 649 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.5919 (tp) REVERT: B 601 ILE cc_start: 0.8559 (mm) cc_final: 0.8042 (pt) REVERT: C 514 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7642 (tmt-80) REVERT: C 516 SER cc_start: 0.8581 (m) cc_final: 0.8088 (p) REVERT: C 592 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: D 361 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8165 (pp20) REVERT: D 488 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.6845 (mmt180) REVERT: D 516 SER cc_start: 0.9510 (m) cc_final: 0.9041 (p) REVERT: D 640 MET cc_start: 0.7868 (mtp) cc_final: 0.7410 (mtm) REVERT: D 664 LYS cc_start: 0.9274 (ttpp) cc_final: 0.9048 (ttpp) REVERT: F 452 ASN cc_start: 0.8600 (m110) cc_final: 0.8137 (m110) REVERT: F 584 HIS cc_start: 0.8676 (m170) cc_final: 0.7943 (t70) REVERT: F 682 GLU cc_start: 0.4394 (pm20) cc_final: 0.4018 (pm20) REVERT: L 82 ARG cc_start: 0.8722 (ptt-90) cc_final: 0.8448 (ptt90) REVERT: L 126 GLU cc_start: 0.8972 (mp0) cc_final: 0.8437 (mp0) outliers start: 40 outliers final: 21 residues processed: 211 average time/residue: 0.4805 time to fit residues: 112.0789 Evaluate side-chains 211 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 496 ASN B 477 ASN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 585 GLN D 651 ASN E 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062376 restraints weight = 34881.860| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.93 r_work: 0.2925 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12439 Z= 0.314 Angle : 0.641 9.229 16915 Z= 0.332 Chirality : 0.046 0.224 1757 Planarity : 0.005 0.036 2227 Dihedral : 5.124 36.989 1660 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.42 % Allowed : 11.64 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1482 helix: -2.28 (0.63), residues: 62 sheet: -0.09 (0.30), residues: 257 loop : -0.44 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 296 TYR 0.018 0.002 TYR L 107 PHE 0.015 0.002 PHE L 70 TRP 0.014 0.002 TRP F 509 HIS 0.009 0.002 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00721 (12437) covalent geometry : angle 0.64100 (16911) SS BOND : bond 0.00337 ( 2) SS BOND : angle 1.38930 ( 4) hydrogen bonds : bond 0.03239 ( 249) hydrogen bonds : angle 5.61781 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.504 Fit side-chains REVERT: A 488 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.5866 (mmt180) REVERT: A 626 ASP cc_start: 0.8502 (m-30) cc_final: 0.8212 (m-30) REVERT: A 649 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4917 (tp) REVERT: C 486 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9043 (tt0) REVERT: C 514 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7715 (mmt180) REVERT: C 592 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: D 361 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8113 (pp20) REVERT: D 488 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.6601 (mpt180) REVERT: D 516 SER cc_start: 0.9527 (m) cc_final: 0.9062 (p) REVERT: D 640 MET cc_start: 0.7973 (mtp) cc_final: 0.7504 (mtm) REVERT: D 664 LYS cc_start: 0.9263 (ttpp) cc_final: 0.9034 (ttpp) REVERT: F 452 ASN cc_start: 0.8563 (m110) cc_final: 0.8100 (m110) REVERT: F 682 GLU cc_start: 0.4493 (pm20) cc_final: 0.3664 (pm20) REVERT: L 104 GLU cc_start: 0.9077 (tt0) cc_final: 0.8672 (tp30) outliers start: 45 outliers final: 25 residues processed: 201 average time/residue: 0.4970 time to fit residues: 110.4732 Evaluate side-chains 196 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 585 GLN E 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064641 restraints weight = 34282.836| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.92 r_work: 0.2974 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12439 Z= 0.127 Angle : 0.561 9.564 16915 Z= 0.283 Chirality : 0.042 0.237 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.672 34.063 1660 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 13.62 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1482 helix: -2.29 (0.61), residues: 72 sheet: 0.43 (0.30), residues: 237 loop : -0.33 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 124 TYR 0.014 0.001 TYR C 484 PHE 0.012 0.001 PHE H 97 TRP 0.012 0.001 TRP F 509 HIS 0.005 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00294 (12437) covalent geometry : angle 0.56037 (16911) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.06834 ( 4) hydrogen bonds : bond 0.02650 ( 249) hydrogen bonds : angle 5.19729 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.487 Fit side-chains REVERT: A 488 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.5819 (mmt180) REVERT: A 626 ASP cc_start: 0.8476 (m-30) cc_final: 0.8173 (m-30) REVERT: A 649 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.4937 (tp) REVERT: C 514 ARG cc_start: 0.8084 (mtm180) cc_final: 0.7616 (tmt-80) REVERT: C 516 SER cc_start: 0.8647 (m) cc_final: 0.8102 (p) REVERT: C 532 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8095 (p0) REVERT: C 592 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: D 361 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8123 (pp20) REVERT: D 398 GLU cc_start: 0.4671 (tm-30) cc_final: 0.4326 (tm-30) REVERT: D 488 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.6559 (mmt180) REVERT: D 516 SER cc_start: 0.9501 (m) cc_final: 0.9018 (p) REVERT: D 640 MET cc_start: 0.7925 (mtp) cc_final: 0.7443 (mtm) REVERT: F 452 ASN cc_start: 0.8540 (m110) cc_final: 0.8060 (m110) REVERT: F 682 GLU cc_start: 0.4252 (pm20) cc_final: 0.3668 (pm20) REVERT: H 127 ASP cc_start: 0.8547 (m-30) cc_final: 0.8184 (m-30) REVERT: L 33 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8895 (p) REVERT: L 81 ASP cc_start: 0.8715 (t0) cc_final: 0.8499 (t0) REVERT: L 104 GLU cc_start: 0.9036 (tt0) cc_final: 0.8616 (mm-30) REVERT: L 126 GLU cc_start: 0.8936 (mp0) cc_final: 0.8384 (mp0) outliers start: 28 outliers final: 13 residues processed: 205 average time/residue: 0.4928 time to fit residues: 111.7726 Evaluate side-chains 200 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 141 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 486 GLN C 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065610 restraints weight = 34031.088| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.91 r_work: 0.2997 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12439 Z= 0.110 Angle : 0.552 9.893 16915 Z= 0.277 Chirality : 0.042 0.232 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.386 31.989 1660 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.98 % Allowed : 13.93 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1482 helix: -2.28 (0.66), residues: 66 sheet: 0.28 (0.30), residues: 257 loop : -0.26 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 124 TYR 0.013 0.001 TYR C 484 PHE 0.013 0.001 PHE A 662 TRP 0.018 0.001 TRP A 595 HIS 0.005 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00255 (12437) covalent geometry : angle 0.55178 (16911) SS BOND : bond 0.00288 ( 2) SS BOND : angle 1.00812 ( 4) hydrogen bonds : bond 0.02480 ( 249) hydrogen bonds : angle 4.97919 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.452 Fit side-chains REVERT: A 271 ASP cc_start: 0.8902 (m-30) cc_final: 0.8397 (m-30) REVERT: A 488 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.5815 (mmt180) REVERT: A 626 ASP cc_start: 0.8490 (m-30) cc_final: 0.8199 (m-30) REVERT: A 649 ILE cc_start: 0.5526 (OUTLIER) cc_final: 0.5044 (tp) REVERT: C 514 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7633 (tmt-80) REVERT: C 516 SER cc_start: 0.8640 (m) cc_final: 0.8091 (p) REVERT: C 532 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8126 (p0) REVERT: C 592 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: D 361 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8135 (pp20) REVERT: D 398 GLU cc_start: 0.4656 (tm-30) cc_final: 0.4296 (tm-30) REVERT: D 488 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.6913 (mmt180) REVERT: D 516 SER cc_start: 0.9475 (m) cc_final: 0.8998 (p) REVERT: D 640 MET cc_start: 0.7935 (mtp) cc_final: 0.7458 (mtm) REVERT: F 452 ASN cc_start: 0.8556 (m110) cc_final: 0.8061 (m110) REVERT: F 584 HIS cc_start: 0.8644 (m170) cc_final: 0.7939 (t70) REVERT: F 682 GLU cc_start: 0.4272 (pm20) cc_final: 0.3694 (pm20) REVERT: H 97 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7816 (t80) REVERT: H 127 ASP cc_start: 0.8554 (m-30) cc_final: 0.8189 (m-30) REVERT: L 81 ASP cc_start: 0.8723 (t0) cc_final: 0.8493 (t0) REVERT: L 104 GLU cc_start: 0.9008 (tt0) cc_final: 0.8567 (tp30) REVERT: L 126 GLU cc_start: 0.8935 (mp0) cc_final: 0.8385 (mp0) outliers start: 26 outliers final: 14 residues processed: 209 average time/residue: 0.4931 time to fit residues: 113.9513 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 0.0070 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 99 optimal weight: 0.0020 chunk 133 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 1.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066664 restraints weight = 33768.177| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.91 r_work: 0.3020 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12439 Z= 0.097 Angle : 0.544 9.327 16915 Z= 0.272 Chirality : 0.041 0.231 1757 Planarity : 0.004 0.033 2227 Dihedral : 4.163 30.926 1660 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 15.07 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1482 helix: -2.16 (0.67), residues: 66 sheet: 0.47 (0.30), residues: 257 loop : -0.23 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 124 TYR 0.012 0.001 TYR C 484 PHE 0.013 0.001 PHE H 97 TRP 0.014 0.001 TRP F 509 HIS 0.005 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00227 (12437) covalent geometry : angle 0.54386 (16911) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.01475 ( 4) hydrogen bonds : bond 0.02407 ( 249) hydrogen bonds : angle 4.77567 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.466 Fit side-chains REVERT: A 271 ASP cc_start: 0.8929 (m-30) cc_final: 0.8405 (m-30) REVERT: A 488 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.5827 (mmt180) REVERT: A 626 ASP cc_start: 0.8491 (m-30) cc_final: 0.8189 (m-30) REVERT: C 514 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7599 (tmt-80) REVERT: C 516 SER cc_start: 0.8640 (m) cc_final: 0.8105 (p) REVERT: C 568 THR cc_start: 0.9393 (p) cc_final: 0.9016 (t) REVERT: C 592 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: D 361 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8119 (pp20) REVERT: D 398 GLU cc_start: 0.4734 (tm-30) cc_final: 0.4379 (tm-30) REVERT: D 486 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8670 (mt0) REVERT: D 488 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.6936 (mmt180) REVERT: D 516 SER cc_start: 0.9480 (m) cc_final: 0.8991 (p) REVERT: F 452 ASN cc_start: 0.8543 (m110) cc_final: 0.8056 (m110) REVERT: F 514 ARG cc_start: 0.4584 (mmt180) cc_final: 0.3350 (tmt170) REVERT: F 584 HIS cc_start: 0.8629 (m170) cc_final: 0.7958 (t70) REVERT: F 682 GLU cc_start: 0.4274 (pm20) cc_final: 0.3764 (pm20) REVERT: H 97 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7824 (t80) REVERT: H 127 ASP cc_start: 0.8556 (m-30) cc_final: 0.8259 (m-30) REVERT: L 104 GLU cc_start: 0.8995 (tt0) cc_final: 0.8615 (tp30) REVERT: L 126 GLU cc_start: 0.8862 (mp0) cc_final: 0.8597 (mp0) REVERT: L 127 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.8884 (m) outliers start: 20 outliers final: 10 residues processed: 207 average time/residue: 0.5099 time to fit residues: 116.3008 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 142 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 0.0770 chunk 98 optimal weight: 0.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067612 restraints weight = 33574.679| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.92 r_work: 0.3041 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12439 Z= 0.091 Angle : 0.548 9.989 16915 Z= 0.272 Chirality : 0.041 0.214 1757 Planarity : 0.004 0.034 2227 Dihedral : 3.979 30.660 1660 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.22 % Allowed : 15.53 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1482 helix: -2.04 (0.68), residues: 66 sheet: 0.89 (0.31), residues: 237 loop : -0.19 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 57 TYR 0.012 0.001 TYR H 71 PHE 0.015 0.001 PHE H 97 TRP 0.015 0.001 TRP A 595 HIS 0.005 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00212 (12437) covalent geometry : angle 0.54838 (16911) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.86582 ( 4) hydrogen bonds : bond 0.02295 ( 249) hydrogen bonds : angle 4.64944 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.499 Fit side-chains REVERT: A 271 ASP cc_start: 0.8905 (m-30) cc_final: 0.8381 (m-30) REVERT: A 488 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.5799 (mmt180) REVERT: A 626 ASP cc_start: 0.8497 (m-30) cc_final: 0.8190 (m-30) REVERT: C 449 LYS cc_start: 0.8119 (mttt) cc_final: 0.7727 (mptt) REVERT: C 514 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7608 (tmt-80) REVERT: C 516 SER cc_start: 0.8701 (m) cc_final: 0.8214 (p) REVERT: C 568 THR cc_start: 0.9391 (p) cc_final: 0.9045 (t) REVERT: C 592 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: D 361 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8134 (pp20) REVERT: D 398 GLU cc_start: 0.4853 (tm-30) cc_final: 0.4498 (tm-30) REVERT: D 486 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8751 (mt0) REVERT: D 488 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.6960 (mmt180) REVERT: D 516 SER cc_start: 0.9508 (m) cc_final: 0.9017 (p) REVERT: F 452 ASN cc_start: 0.8563 (m110) cc_final: 0.8068 (m110) REVERT: F 514 ARG cc_start: 0.4625 (mmt180) cc_final: 0.3379 (tmt170) REVERT: F 584 HIS cc_start: 0.8618 (m170) cc_final: 0.7951 (t70) REVERT: F 682 GLU cc_start: 0.4250 (pm20) cc_final: 0.3715 (pm20) REVERT: H 62 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8869 (mttp) REVERT: H 127 ASP cc_start: 0.8538 (m-30) cc_final: 0.8177 (m-30) REVERT: L 104 GLU cc_start: 0.8957 (tt0) cc_final: 0.8612 (tp30) REVERT: L 127 VAL cc_start: 0.9568 (OUTLIER) cc_final: 0.8949 (m) outliers start: 16 outliers final: 11 residues processed: 212 average time/residue: 0.4802 time to fit residues: 112.6833 Evaluate side-chains 201 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.078654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065062 restraints weight = 34287.671| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.92 r_work: 0.2985 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12439 Z= 0.178 Angle : 0.586 9.606 16915 Z= 0.297 Chirality : 0.042 0.212 1757 Planarity : 0.004 0.033 2227 Dihedral : 4.335 33.405 1660 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.99 % Allowed : 16.67 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1482 helix: -2.18 (0.66), residues: 66 sheet: 0.75 (0.31), residues: 237 loop : -0.22 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.016 0.001 TYR C 484 PHE 0.014 0.001 PHE H 97 TRP 0.018 0.001 TRP A 595 HIS 0.009 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00413 (12437) covalent geometry : angle 0.58601 (16911) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.99351 ( 4) hydrogen bonds : bond 0.02627 ( 249) hydrogen bonds : angle 5.00584 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.508 Fit side-chains REVERT: A 271 ASP cc_start: 0.8894 (m-30) cc_final: 0.8381 (m-30) REVERT: A 488 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.5821 (mmt180) REVERT: A 626 ASP cc_start: 0.8485 (m-30) cc_final: 0.8198 (m-30) REVERT: B 451 ILE cc_start: 0.9333 (pt) cc_final: 0.9102 (pp) REVERT: B 601 ILE cc_start: 0.8534 (tp) cc_final: 0.8198 (pt) REVERT: C 436 MET cc_start: 0.9211 (pmm) cc_final: 0.8953 (pmm) REVERT: C 514 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7594 (tmt-80) REVERT: C 516 SER cc_start: 0.8675 (m) cc_final: 0.8181 (p) REVERT: D 361 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8117 (pp20) REVERT: D 488 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.6904 (mmt180) REVERT: D 516 SER cc_start: 0.9538 (m) cc_final: 0.9067 (p) REVERT: F 452 ASN cc_start: 0.8548 (m110) cc_final: 0.8049 (m110) REVERT: F 514 ARG cc_start: 0.4457 (mmt180) cc_final: 0.3218 (tmt170) REVERT: F 584 HIS cc_start: 0.8674 (m170) cc_final: 0.7897 (t70) REVERT: F 682 GLU cc_start: 0.4320 (pm20) cc_final: 0.3707 (pm20) REVERT: H 127 ASP cc_start: 0.8483 (m-30) cc_final: 0.8110 (m-30) REVERT: L 104 GLU cc_start: 0.9017 (tt0) cc_final: 0.8634 (tp30) outliers start: 13 outliers final: 14 residues processed: 195 average time/residue: 0.5033 time to fit residues: 108.4568 Evaluate side-chains 197 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 147 optimal weight: 0.0030 chunk 119 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN C 585 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.066151 restraints weight = 33843.369| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.91 r_work: 0.3010 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12439 Z= 0.113 Angle : 0.574 9.734 16915 Z= 0.287 Chirality : 0.041 0.216 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.191 33.111 1660 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.22 % Allowed : 16.67 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1482 helix: -2.05 (0.68), residues: 66 sheet: 0.54 (0.31), residues: 257 loop : -0.18 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 485 TYR 0.016 0.001 TYR H 72 PHE 0.012 0.001 PHE H 97 TRP 0.015 0.001 TRP A 595 HIS 0.006 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00266 (12437) covalent geometry : angle 0.57433 (16911) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.90615 ( 4) hydrogen bonds : bond 0.02417 ( 249) hydrogen bonds : angle 4.86454 ( 597) =============================================================================== Job complete usr+sys time: 4727.55 seconds wall clock time: 81 minutes 16.96 seconds (4876.96 seconds total)