Starting phenix.real_space_refine on Wed May 14 14:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6t_44277/05_2025/9b6t_44277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6t_44277/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6t_44277/05_2025/9b6t_44277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6t_44277/05_2025/9b6t_44277.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6t_44277/05_2025/9b6t_44277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6t_44277/05_2025/9b6t_44277.cif" } resolution = 2.54 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 ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.05, per 1000 atoms: 0.58 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: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.68 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: 4.18 Time building geometry restraints manager: 3.11 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.750 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- 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 : 16.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), 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 TRP 0.026 0.003 TRP A 281 HIS 0.009 0.002 HIS F 292 PHE 0.031 0.002 PHE H 97 TYR 0.031 0.003 TYR H 71 ARG 0.010 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.22323 ( 249) hydrogen bonds : angle 9.26031 ( 597) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.40871 ( 4) covalent geometry : bond 0.00933 (12437) covalent geometry : angle 0.94301 (16911) *********************** 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 : 1.316 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: 1.0228 time to fit residues: 300.2042 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 : 1.486 ------------------------------------------------------------------------------- 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 128 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 B 585 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065342 restraints weight = 34079.553| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.89 r_work: 0.2989 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1794 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= 0.172 Angle : 0.614 6.373 16915 Z= 0.323 Chirality : 0.044 0.167 1757 Planarity : 0.004 0.038 2227 Dihedral : 5.268 36.364 1663 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.05 % Allowed : 9.89 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.94 (0.19), residues: 1482 helix: -2.76 (0.53), residues: 72 sheet: -0.33 (0.28), residues: 257 loop : -0.55 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 509 HIS 0.008 0.002 HIS D 255 PHE 0.017 0.002 PHE L 70 TYR 0.026 0.002 TYR H 71 ARG 0.007 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 249) hydrogen bonds : angle 6.25518 ( 597) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.98581 ( 4) covalent geometry : bond 0.00390 (12437) covalent geometry : angle 0.61344 (16911) *********************** 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 247 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8195 (ttp-170) cc_final: 0.5764 (mmt180) REVERT: A 595 TRP cc_start: 0.8529 (m100) cc_final: 0.8280 (m100) REVERT: A 626 ASP cc_start: 0.8539 (m-30) cc_final: 0.8202 (m-30) REVERT: B 483 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8264 (m) REVERT: B 601 ILE cc_start: 0.8628 (mm) cc_final: 0.8369 (pt) REVERT: C 471 MET cc_start: 0.9000 (mtm) cc_final: 0.8776 (ttm) REVERT: C 514 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7866 (tmt-80) REVERT: C 516 SER cc_start: 0.8470 (m) cc_final: 0.8078 (p) REVERT: D 361 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8138 (pp20) REVERT: D 488 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.6857 (mmt180) REVERT: D 516 SER cc_start: 0.9481 (m) cc_final: 0.9065 (p) REVERT: D 640 MET cc_start: 0.7905 (mtp) cc_final: 0.7455 (mtm) REVERT: E 574 THR cc_start: 0.8000 (p) cc_final: 0.7602 (p) REVERT: E 575 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8121 (mm-30) REVERT: F 452 ASN cc_start: 0.8719 (m110) cc_final: 0.8217 (m110) REVERT: F 584 HIS cc_start: 0.8786 (m170) cc_final: 0.7965 (t70) REVERT: L 82 ARG cc_start: 0.8757 (ptt-90) cc_final: 0.8519 (ptt90) outliers start: 27 outliers final: 11 residues processed: 232 average time/residue: 0.9432 time to fit residues: 243.1194 Evaluate side-chains 198 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 86 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 101 optimal weight: 0.0030 chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 overall best weight: 6.7998 ------------------------------------------------------------------------------- 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 B 585 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064097 restraints weight = 34594.786| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.91 r_work: 0.2962 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12439 Z= 0.222 Angle : 0.607 10.314 16915 Z= 0.312 Chirality : 0.044 0.244 1757 Planarity : 0.004 0.036 2227 Dihedral : 5.043 33.202 1660 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.74 % Allowed : 10.50 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.69 (0.20), residues: 1482 helix: -2.54 (0.56), residues: 72 sheet: 0.18 (0.30), residues: 237 loop : -0.46 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.010 0.002 HIS H 69 PHE 0.013 0.001 PHE F 367 TYR 0.020 0.002 TYR H 71 ARG 0.005 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 249) hydrogen bonds : angle 5.75218 ( 597) SS BOND : bond 0.00317 ( 2) SS BOND : angle 1.04923 ( 4) covalent geometry : bond 0.00509 (12437) covalent geometry : angle 0.60664 (16911) *********************** 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 229 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.5788 (mmt180) REVERT: A 595 TRP cc_start: 0.8477 (m100) cc_final: 0.8243 (m100) REVERT: A 601 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 626 ASP cc_start: 0.8568 (m-30) cc_final: 0.8218 (m-30) REVERT: B 601 ILE cc_start: 0.8578 (mm) cc_final: 0.8090 (pt) REVERT: C 471 MET cc_start: 0.9036 (mtm) cc_final: 0.8781 (ttm) REVERT: C 514 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7723 (tmt-80) REVERT: C 592 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: D 361 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8200 (pp20) REVERT: D 488 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.6837 (mmt180) REVERT: D 516 SER cc_start: 0.9494 (m) cc_final: 0.9057 (p) REVERT: D 640 MET cc_start: 0.7935 (mtp) cc_final: 0.7472 (mtm) REVERT: D 664 LYS cc_start: 0.9283 (ttpp) cc_final: 0.9082 (ttpp) REVERT: E 575 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8063 (mm-30) REVERT: F 452 ASN cc_start: 0.8640 (m110) cc_final: 0.8193 (m110) REVERT: F 514 ARG cc_start: 0.4500 (OUTLIER) cc_final: 0.4281 (mmt180) REVERT: F 584 HIS cc_start: 0.8788 (m170) cc_final: 0.7960 (t70) REVERT: F 682 GLU cc_start: 0.4539 (pm20) cc_final: 0.4127 (pm20) REVERT: L 82 ARG cc_start: 0.8815 (ptt-90) cc_final: 0.8494 (ptt90) REVERT: L 126 GLU cc_start: 0.8976 (mp0) cc_final: 0.8457 (mp0) outliers start: 36 outliers final: 19 residues processed: 209 average time/residue: 0.9681 time to fit residues: 224.1256 Evaluate side-chains 203 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 F residue 514 ARG 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 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 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 130 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 84 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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 24 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064909 restraints weight = 33816.831| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.89 r_work: 0.2977 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12439 Z= 0.154 Angle : 0.565 9.396 16915 Z= 0.289 Chirality : 0.042 0.240 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.746 31.855 1660 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.59 % Allowed : 11.80 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.51 (0.20), residues: 1482 helix: -2.40 (0.58), residues: 72 sheet: 0.30 (0.30), residues: 237 loop : -0.33 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 509 HIS 0.005 0.001 HIS H 69 PHE 0.012 0.001 PHE L 70 TYR 0.016 0.001 TYR H 71 ARG 0.004 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 249) hydrogen bonds : angle 5.40531 ( 597) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.88082 ( 4) covalent geometry : bond 0.00355 (12437) covalent geometry : angle 0.56512 (16911) *********************** 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 232 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.5804 (mmt180) REVERT: A 595 TRP cc_start: 0.8448 (m100) cc_final: 0.8228 (m100) REVERT: A 626 ASP cc_start: 0.8533 (m-30) cc_final: 0.8200 (m-30) REVERT: A 649 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5959 (tp) REVERT: C 514 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7630 (tmt-80) REVERT: C 516 SER cc_start: 0.8577 (m) cc_final: 0.8086 (p) REVERT: C 592 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: D 361 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8152 (pp20) REVERT: D 398 GLU cc_start: 0.4853 (tm-30) cc_final: 0.4498 (tm-30) REVERT: D 488 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.6864 (mmt180) REVERT: D 516 SER cc_start: 0.9508 (m) cc_final: 0.9049 (p) REVERT: D 640 MET cc_start: 0.7898 (mtp) cc_final: 0.7438 (mtm) REVERT: F 452 ASN cc_start: 0.8593 (m110) cc_final: 0.8129 (m110) REVERT: F 584 HIS cc_start: 0.8668 (m170) cc_final: 0.7951 (t70) REVERT: F 682 GLU cc_start: 0.4501 (pm20) cc_final: 0.4030 (pm20) REVERT: L 82 ARG cc_start: 0.8730 (ptt-90) cc_final: 0.8442 (ptt90) REVERT: L 106 ASP cc_start: 0.9116 (m-30) cc_final: 0.8911 (m-30) REVERT: L 126 GLU cc_start: 0.8968 (mp0) cc_final: 0.8518 (mp0) outliers start: 34 outliers final: 18 residues processed: 209 average time/residue: 0.9663 time to fit residues: 223.7641 Evaluate side-chains 207 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 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 C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 82 LEU 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 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 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 29 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN C 495 GLN C 585 GLN D 651 ASN ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064180 restraints weight = 34183.149| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.91 r_work: 0.2964 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12439 Z= 0.186 Angle : 0.569 9.283 16915 Z= 0.290 Chirality : 0.043 0.234 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.733 33.732 1660 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.12 % Allowed : 11.49 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.44 (0.20), residues: 1482 helix: -2.37 (0.59), residues: 72 sheet: 0.37 (0.30), residues: 237 loop : -0.29 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 509 HIS 0.008 0.001 HIS H 69 PHE 0.013 0.001 PHE L 70 TYR 0.015 0.001 TYR C 484 ARG 0.004 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02817 ( 249) hydrogen bonds : angle 5.26239 ( 597) SS BOND : bond 0.00282 ( 2) SS BOND : angle 1.03284 ( 4) covalent geometry : bond 0.00430 (12437) covalent geometry : angle 0.56876 (16911) *********************** 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 230 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.347 Fit side-chains REVERT: A 488 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.5840 (mmt180) REVERT: A 626 ASP cc_start: 0.8523 (m-30) cc_final: 0.8196 (m-30) REVERT: A 649 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5463 (tp) REVERT: C 486 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8925 (tt0) REVERT: C 514 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7624 (tmt-80) REVERT: C 516 SER cc_start: 0.8602 (m) cc_final: 0.8103 (p) REVERT: C 532 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8107 (p0) REVERT: C 592 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: D 361 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8185 (pp20) REVERT: D 488 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7014 (mpt180) REVERT: D 516 SER cc_start: 0.9498 (m) cc_final: 0.9052 (p) REVERT: D 640 MET cc_start: 0.7956 (mtp) cc_final: 0.7485 (mtm) REVERT: F 452 ASN cc_start: 0.8542 (m110) cc_final: 0.8060 (m110) REVERT: F 514 ARG cc_start: 0.4490 (OUTLIER) cc_final: 0.4273 (mmt180) REVERT: F 584 HIS cc_start: 0.8667 (m170) cc_final: 0.7982 (t70) REVERT: F 682 GLU cc_start: 0.4445 (pm20) cc_final: 0.3878 (pm20) REVERT: L 81 ASP cc_start: 0.8728 (t0) cc_final: 0.8514 (t0) REVERT: L 104 GLU cc_start: 0.9034 (tt0) cc_final: 0.8660 (tp30) REVERT: L 126 GLU cc_start: 0.8991 (mp0) cc_final: 0.8497 (mp0) outliers start: 41 outliers final: 23 residues processed: 207 average time/residue: 0.9412 time to fit residues: 216.4008 Evaluate side-chains 209 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 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 F residue 514 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 50 SER 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 45 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 GLN L 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.063181 restraints weight = 34903.182| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.93 r_work: 0.2940 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12439 Z= 0.254 Angle : 0.607 9.419 16915 Z= 0.311 Chirality : 0.044 0.230 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.912 35.073 1660 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.35 % Allowed : 12.10 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.62 (0.21), residues: 1482 helix: -2.45 (0.58), residues: 72 sheet: 0.03 (0.30), residues: 257 loop : -0.37 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 509 HIS 0.009 0.002 HIS H 69 PHE 0.013 0.001 PHE L 70 TYR 0.016 0.002 TYR L 107 ARG 0.004 0.001 ARG F 296 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 249) hydrogen bonds : angle 5.39535 ( 597) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.26580 ( 4) covalent geometry : bond 0.00587 (12437) covalent geometry : angle 0.60709 (16911) *********************** 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 226 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 1.325 Fit side-chains REVERT: A 488 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.5825 (mmt180) REVERT: A 580 VAL cc_start: 0.8965 (t) cc_final: 0.8740 (t) REVERT: A 601 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 626 ASP cc_start: 0.8500 (m-30) cc_final: 0.8202 (m-30) REVERT: A 649 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.4850 (tp) REVERT: C 486 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (tt0) REVERT: C 514 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7605 (tmt-80) REVERT: C 532 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (p0) REVERT: D 361 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8130 (pp20) REVERT: D 488 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.6501 (mmt180) REVERT: D 516 SER cc_start: 0.9500 (m) cc_final: 0.9029 (p) REVERT: D 640 MET cc_start: 0.7961 (mtp) cc_final: 0.7488 (mtm) REVERT: F 452 ASN cc_start: 0.8514 (m110) cc_final: 0.8034 (m110) REVERT: F 514 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.4252 (mmt180) REVERT: F 682 GLU cc_start: 0.4406 (pm20) cc_final: 0.3516 (pm20) REVERT: H 127 ASP cc_start: 0.8631 (m-30) cc_final: 0.8278 (m-30) REVERT: L 104 GLU cc_start: 0.9063 (tt0) cc_final: 0.8702 (tp30) outliers start: 44 outliers final: 22 residues processed: 203 average time/residue: 0.9261 time to fit residues: 208.9097 Evaluate side-chains 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 VAL 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 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 F residue 514 ARG 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 39 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 63 THR 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 124 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 114 optimal weight: 0.5980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.064709 restraints weight = 34263.204| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.93 r_work: 0.2976 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12439 Z= 0.132 Angle : 0.568 9.822 16915 Z= 0.286 Chirality : 0.042 0.238 1757 Planarity : 0.004 0.033 2227 Dihedral : 4.554 33.379 1660 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 13.77 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.48 (0.21), residues: 1482 helix: -2.28 (0.61), residues: 72 sheet: 0.22 (0.30), residues: 257 loop : -0.30 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 509 HIS 0.006 0.001 HIS H 69 PHE 0.013 0.001 PHE A 662 TYR 0.013 0.001 TYR C 484 ARG 0.003 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.02593 ( 249) hydrogen bonds : angle 5.10187 ( 597) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.05208 ( 4) covalent geometry : bond 0.00307 (12437) covalent geometry : angle 0.56799 (16911) *********************** 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 220 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.439 Fit side-chains REVERT: A 488 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.5822 (mmt180) REVERT: A 601 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7337 (mp) REVERT: A 626 ASP cc_start: 0.8478 (m-30) cc_final: 0.8159 (m-30) REVERT: A 640 MET cc_start: 0.7279 (mmt) cc_final: 0.6536 (mmt) REVERT: A 649 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.4893 (tp) REVERT: C 514 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7593 (tmt-80) REVERT: C 516 SER cc_start: 0.8630 (m) cc_final: 0.8102 (p) REVERT: C 532 ASP cc_start: 0.8387 (m-30) cc_final: 0.8173 (p0) REVERT: C 592 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: D 361 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8133 (pp20) REVERT: D 398 GLU cc_start: 0.4749 (tm-30) cc_final: 0.4332 (tm-30) REVERT: D 488 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.6525 (mmt180) REVERT: D 516 SER cc_start: 0.9475 (m) cc_final: 0.8993 (p) REVERT: D 640 MET cc_start: 0.7925 (mtp) cc_final: 0.7453 (mtm) REVERT: F 452 ASN cc_start: 0.8524 (m110) cc_final: 0.8040 (m110) REVERT: F 514 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.4119 (mmt180) REVERT: F 682 GLU cc_start: 0.4466 (pm20) cc_final: 0.3859 (pm20) REVERT: H 127 ASP cc_start: 0.8574 (m-30) cc_final: 0.8211 (m-30) REVERT: L 104 GLU cc_start: 0.9029 (tt0) cc_final: 0.8664 (pt0) REVERT: L 126 GLU cc_start: 0.8960 (mp0) cc_final: 0.8397 (mp0) outliers start: 27 outliers final: 15 residues processed: 208 average time/residue: 1.0160 time to fit residues: 234.1984 Evaluate side-chains 197 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 601 ILE 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 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 F residue 514 ARG 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 L residue 45 SER 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 3 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 46 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN L 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.080697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067151 restraints weight = 34095.872| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.93 r_work: 0.3028 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3093 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= 0.089 Angle : 0.554 9.444 16915 Z= 0.276 Chirality : 0.041 0.234 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.134 32.035 1660 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.60 % Allowed : 14.76 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.29 (0.21), residues: 1482 helix: -2.14 (0.66), residues: 66 sheet: 0.46 (0.31), residues: 257 loop : -0.21 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 509 HIS 0.004 0.001 HIS H 69 PHE 0.015 0.001 PHE A 662 TYR 0.012 0.001 TYR L 108 ARG 0.004 0.000 ARG L 124 Details of bonding type rmsd hydrogen bonds : bond 0.02369 ( 249) hydrogen bonds : angle 4.71213 ( 597) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.15038 ( 4) covalent geometry : bond 0.00203 (12437) covalent geometry : angle 0.55416 (16911) *********************** 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 225 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.867 Fit side-chains REVERT: A 271 ASP cc_start: 0.8954 (m-30) cc_final: 0.8447 (m-30) REVERT: A 488 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.5852 (mmt180) REVERT: A 601 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 626 ASP cc_start: 0.8493 (m-30) cc_final: 0.8192 (m-30) REVERT: C 242 THR cc_start: 0.8389 (m) cc_final: 0.8134 (p) REVERT: C 449 LYS cc_start: 0.8110 (mttt) cc_final: 0.7702 (mptt) REVERT: C 514 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7601 (tmt-80) REVERT: C 516 SER cc_start: 0.8684 (m) cc_final: 0.8150 (p) REVERT: C 568 THR cc_start: 0.9385 (p) cc_final: 0.9034 (t) REVERT: C 592 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: D 361 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8116 (pp20) REVERT: D 398 GLU cc_start: 0.4931 (tm-30) cc_final: 0.4519 (tm-30) REVERT: D 486 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8680 (mt0) REVERT: D 488 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.6944 (mmt180) REVERT: D 516 SER cc_start: 0.9450 (m) cc_final: 0.9047 (t) REVERT: F 452 ASN cc_start: 0.8555 (m110) cc_final: 0.8069 (m110) REVERT: F 514 ARG cc_start: 0.4423 (OUTLIER) cc_final: 0.4212 (mmt180) REVERT: F 584 HIS cc_start: 0.8652 (m170) cc_final: 0.7959 (t70) REVERT: F 682 GLU cc_start: 0.4266 (pm20) cc_final: 0.3768 (pm20) REVERT: H 97 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7780 (t80) REVERT: H 127 ASP cc_start: 0.8500 (m-30) cc_final: 0.8203 (m-30) REVERT: L 104 GLU cc_start: 0.9020 (tt0) cc_final: 0.8646 (mm-30) REVERT: L 124 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8857 (tmm-80) REVERT: L 126 GLU cc_start: 0.8926 (mp0) cc_final: 0.8337 (mp0) REVERT: L 127 VAL cc_start: 0.9549 (OUTLIER) cc_final: 0.8799 (m) outliers start: 21 outliers final: 9 residues processed: 213 average time/residue: 1.0031 time to fit residues: 236.3928 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 444 LEU 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 F residue 514 ARG 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 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065449 restraints weight = 34028.228| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.92 r_work: 0.2994 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12439 Z= 0.141 Angle : 0.566 9.590 16915 Z= 0.285 Chirality : 0.042 0.220 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.268 32.161 1660 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.37 % Allowed : 16.06 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.30 (0.21), residues: 1482 helix: -2.14 (0.67), residues: 66 sheet: 0.43 (0.31), residues: 257 loop : -0.21 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 509 HIS 0.007 0.001 HIS H 69 PHE 0.014 0.001 PHE H 97 TYR 0.014 0.001 TYR C 484 ARG 0.005 0.000 ARG L 124 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 249) hydrogen bonds : angle 4.86075 ( 597) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.98339 ( 4) covalent geometry : bond 0.00330 (12437) covalent geometry : angle 0.56546 (16911) *********************** 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 201 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.8933 (m-30) cc_final: 0.8430 (m-30) REVERT: A 488 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.5829 (mmt180) REVERT: A 601 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 626 ASP cc_start: 0.8513 (m-30) cc_final: 0.8216 (m-30) REVERT: C 514 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7629 (tmt-80) REVERT: C 516 SER cc_start: 0.8704 (m) cc_final: 0.8196 (p) REVERT: D 361 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8125 (pp20) REVERT: D 398 GLU cc_start: 0.4779 (tm-30) cc_final: 0.4435 (tm-30) REVERT: D 488 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.6917 (mmt180) REVERT: D 516 SER cc_start: 0.9474 (m) cc_final: 0.9022 (p) REVERT: F 452 ASN cc_start: 0.8554 (m110) cc_final: 0.8064 (m110) REVERT: F 514 ARG cc_start: 0.4499 (OUTLIER) cc_final: 0.4193 (mmt180) REVERT: F 584 HIS cc_start: 0.8669 (m170) cc_final: 0.7906 (t70) REVERT: F 682 GLU cc_start: 0.4475 (pm20) cc_final: 0.3876 (pm20) REVERT: H 24 GLN cc_start: 0.9033 (tp40) cc_final: 0.8794 (tp-100) REVERT: H 127 ASP cc_start: 0.8555 (m-30) cc_final: 0.8249 (m-30) REVERT: L 126 GLU cc_start: 0.8855 (mp0) cc_final: 0.8627 (mp0) outliers start: 18 outliers final: 13 residues processed: 192 average time/residue: 0.9425 time to fit residues: 200.5412 Evaluate side-chains 194 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain F residue 514 ARG 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 39 THR Chi-restraints excluded: chain L residue 45 SER 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 90 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 376 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.077171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063579 restraints weight = 34399.529| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.88 r_work: 0.2948 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12439 Z= 0.269 Angle : 0.634 10.255 16915 Z= 0.325 Chirality : 0.044 0.225 1757 Planarity : 0.004 0.032 2227 Dihedral : 4.738 35.363 1660 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 16.06 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.48 (0.21), residues: 1482 helix: -2.02 (0.64), residues: 68 sheet: 0.19 (0.31), residues: 259 loop : -0.32 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 509 HIS 0.011 0.002 HIS H 69 PHE 0.015 0.002 PHE C 284 TYR 0.020 0.002 TYR H 72 ARG 0.004 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 249) hydrogen bonds : angle 5.30653 ( 597) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.15156 ( 4) covalent geometry : bond 0.00618 (12437) covalent geometry : angle 0.63413 (16911) ********************** 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 195 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 262 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8624 (p0) REVERT: A 488 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.5836 (mmt180) REVERT: A 601 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7365 (mp) REVERT: A 626 ASP cc_start: 0.8491 (m-30) cc_final: 0.8219 (m-30) REVERT: C 514 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7613 (mmt180) REVERT: C 516 SER cc_start: 0.8661 (m) cc_final: 0.8164 (p) REVERT: D 361 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8095 (pp20) REVERT: D 488 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.6518 (mmt180) REVERT: D 516 SER cc_start: 0.9492 (m) cc_final: 0.9012 (p) REVERT: D 640 MET cc_start: 0.8507 (mtp) cc_final: 0.8104 (mtm) REVERT: F 452 ASN cc_start: 0.8521 (m110) cc_final: 0.8014 (m110) REVERT: F 514 ARG cc_start: 0.4429 (OUTLIER) cc_final: 0.4146 (mmt180) REVERT: F 682 GLU cc_start: 0.4338 (pm20) cc_final: 0.3469 (pm20) REVERT: H 24 GLN cc_start: 0.9074 (tp40) cc_final: 0.8783 (tp-100) REVERT: H 127 ASP cc_start: 0.8637 (m-30) cc_final: 0.8283 (m-30) outliers start: 22 outliers final: 14 residues processed: 185 average time/residue: 0.9709 time to fit residues: 199.3369 Evaluate side-chains 189 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 514 ARG 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 39 THR Chi-restraints excluded: chain L residue 45 SER 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 40 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 376 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 ASN ** 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 = 0.3346 r_free = 0.3346 target = 0.077220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063504 restraints weight = 34344.159| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.90 r_work: 0.2948 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 12439 Z= 0.265 Angle : 0.852 59.019 16915 Z= 0.489 Chirality : 0.048 0.868 1757 Planarity : 0.004 0.032 2227 Dihedral : 4.793 35.327 1660 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.37 % Allowed : 16.67 % Favored : 81.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.70 % 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: -0.49 (0.21), residues: 1482 helix: -2.06 (0.64), residues: 68 sheet: 0.18 (0.31), residues: 259 loop : -0.32 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 509 HIS 0.009 0.001 HIS H 69 PHE 0.014 0.001 PHE A 662 TYR 0.018 0.002 TYR C 484 ARG 0.006 0.001 ARG L 124 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 249) hydrogen bonds : angle 5.31309 ( 597) SS BOND : bond 0.00231 ( 2) SS BOND : angle 1.18275 ( 4) covalent geometry : bond 0.00584 (12437) covalent geometry : angle 0.85159 (16911) =============================================================================== Job complete usr+sys time: 8382.18 seconds wall clock time: 144 minutes 53.21 seconds (8693.21 seconds total)