Starting phenix.real_space_refine on Wed Jul 30 02:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6t_44277/07_2025/9b6t_44277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6t_44277/07_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_44277/07_2025/9b6t_44277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6t_44277/07_2025/9b6t_44277.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6t_44277/07_2025/9b6t_44277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6t_44277/07_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-5711/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: 7.20, per 1000 atoms: 0.59 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: 2.49 Conformation dependent library (CDL) restraints added in 1.4 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: 1.48 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: 3.63 Time building geometry restraints manager: 3.03 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: 0.540 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.860 Find NCS groups from input model: 0.260 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- 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 : 1.276 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: 1.0653 time to fit residues: 311.9375 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 : 1.238 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065343 restraints weight = 34079.501| |-----------------------------------------------------------------------------| 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 6.25519 ( 597) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.98580 ( 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 : 2.433 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: 0.8528 (m100) cc_final: 0.8279 (m100) REVERT: A 626 ASP cc_start: 0.8539 (m-30) cc_final: 0.8200 (m-30) REVERT: B 483 SER cc_start: 0.8765 (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: 0.9001 (mtm) cc_final: 0.8776 (ttm) REVERT: C 514 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7866 (tmt-80) REVERT: C 516 SER cc_start: 0.8471 (m) cc_final: 0.8077 (p) REVERT: D 361 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8137 (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: 0.9064 (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: 0.7603 (p) REVERT: E 575 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8123 (mm-30) REVERT: F 452 ASN cc_start: 0.8720 (m110) cc_final: 0.8219 (m110) REVERT: F 584 HIS cc_start: 0.8787 (m170) cc_final: 0.7965 (t70) REVERT: L 82 ARG cc_start: 0.8757 (ptt-90) cc_final: 0.8517 (ptt90) outliers start: 27 outliers final: 11 residues processed: 232 average time/residue: 1.0093 time to fit residues: 259.4162 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 : 1.445 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 101 optimal weight: 0.0020 chunk 124 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- 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 495 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.064729 restraints weight = 34450.895| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.93 r_work: 0.2974 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12439 Z= 0.185 Angle : 0.590 9.826 16915 Z= 0.303 Chirality : 0.043 0.237 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.953 32.627 1660 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 10.73 % 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: -0.63 (0.20), residues: 1482 helix: -2.50 (0.57), residues: 72 sheet: 0.22 (0.30), residues: 237 loop : -0.42 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.008 0.001 HIS H 69 PHE 0.012 0.001 PHE H 97 TYR 0.020 0.002 TYR H 71 ARG 0.005 0.001 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 249) hydrogen bonds : angle 5.71948 ( 597) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.99697 ( 4) covalent geometry : bond 0.00425 (12437) covalent geometry : angle 0.59022 (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: 33 poor density : 196 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.5793 (mmt180) REVERT: A 595 TRP cc_start: 0.8488 (m100) cc_final: 0.8256 (m100) REVERT: A 601 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 626 ASP cc_start: 0.8560 (m-30) cc_final: 0.8275 (m-30) REVERT: B 601 ILE cc_start: 0.8574 (mm) cc_final: 0.8095 (pt) REVERT: C 471 MET cc_start: 0.8990 (mtm) cc_final: 0.8737 (ttm) REVERT: C 514 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7733 (tmt-80) REVERT: C 516 SER cc_start: 0.8537 (m) cc_final: 0.8100 (p) REVERT: C 592 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: D 361 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8199 (pp20) REVERT: D 488 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.6839 (mmt180) REVERT: D 516 SER cc_start: 0.9495 (m) cc_final: 0.9063 (p) REVERT: D 640 MET cc_start: 0.7928 (mtp) cc_final: 0.7471 (mtm) REVERT: E 575 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8094 (mm-30) REVERT: F 452 ASN cc_start: 0.8649 (m110) cc_final: 0.8212 (m110) REVERT: F 514 ARG cc_start: 0.4557 (OUTLIER) cc_final: 0.4332 (mmt180) REVERT: F 584 HIS cc_start: 0.8763 (m170) cc_final: 0.7957 (t70) REVERT: F 682 GLU cc_start: 0.4429 (pm20) cc_final: 0.4119 (pm20) REVERT: L 82 ARG cc_start: 0.8784 (ptt-90) cc_final: 0.8465 (ptt90) REVERT: L 126 GLU cc_start: 0.8972 (mp0) cc_final: 0.8469 (mp0) outliers start: 33 outliers final: 16 residues processed: 209 average time/residue: 1.0375 time to fit residues: 240.3219 Evaluate side-chains 203 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain 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 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- 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 E 585 GLN H 24 GLN ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063040 restraints weight = 34275.767| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.88 r_work: 0.2938 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12439 Z= 0.288 Angle : 0.623 9.443 16915 Z= 0.324 Chirality : 0.045 0.230 1757 Planarity : 0.004 0.036 2227 Dihedral : 5.104 35.388 1660 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.65 % Allowed : 10.43 % Favored : 85.92 % 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: -0.68 (0.20), residues: 1482 helix: -2.55 (0.56), residues: 72 sheet: 0.16 (0.31), residues: 237 loop : -0.45 (0.17), residues: 1173 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 0.015 0.002 PHE L 70 TYR 0.018 0.002 TYR L 107 ARG 0.005 0.001 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 249) hydrogen bonds : angle 5.68494 ( 597) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.16968 ( 4) covalent geometry : bond 0.00662 (12437) covalent geometry : angle 0.62273 (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 227 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 488 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.5799 (mmt180) REVERT: A 626 ASP cc_start: 0.8542 (m-30) cc_final: 0.8225 (m-30) REVERT: A 649 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5479 (tp) REVERT: C 514 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7721 (mmt180) REVERT: C 532 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8077 (p0) REVERT: C 592 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: D 361 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8143 (pp20) REVERT: D 488 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.6513 (mmt180) REVERT: D 516 SER cc_start: 0.9520 (m) cc_final: 0.9066 (p) REVERT: D 640 MET cc_start: 0.7986 (mtp) cc_final: 0.7518 (mtm) REVERT: E 575 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7982 (mm-30) REVERT: F 452 ASN cc_start: 0.8577 (m110) cc_final: 0.8107 (m110) REVERT: F 682 GLU cc_start: 0.4581 (pm20) cc_final: 0.3945 (pm20) REVERT: L 82 ARG cc_start: 0.8766 (ptt-90) cc_final: 0.8536 (ptt90) outliers start: 48 outliers final: 22 residues processed: 202 average time/residue: 1.0404 time to fit residues: 232.1766 Evaluate side-chains 199 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 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 D residue 389 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 127 VAL 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: 5.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 496 ASN C 495 GLN C 585 GLN D 651 ASN E 585 GLN F 608 GLN H 24 GLN L 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.063996 restraints weight = 34101.369| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.90 r_work: 0.2959 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12439 Z= 0.190 Angle : 0.578 9.653 16915 Z= 0.295 Chirality : 0.043 0.233 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.843 34.352 1660 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.36 % Allowed : 12.02 % 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: -0.59 (0.21), residues: 1482 helix: -2.37 (0.59), residues: 72 sheet: 0.03 (0.30), residues: 257 loop : -0.35 (0.18), residues: 1153 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 H 97 TYR 0.016 0.001 TYR C 484 ARG 0.004 0.000 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 249) hydrogen bonds : angle 5.38774 ( 597) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.91315 ( 4) covalent geometry : bond 0.00439 (12437) covalent geometry : angle 0.57796 (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 222 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 262 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8627 (p0) REVERT: A 488 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.5841 (mmt180) REVERT: A 626 ASP cc_start: 0.8527 (m-30) cc_final: 0.8215 (m-30) REVERT: A 649 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.4940 (tp) REVERT: C 486 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: C 514 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7641 (tmt-80) REVERT: C 532 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (p0) REVERT: C 592 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: D 361 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8122 (pp20) REVERT: D 488 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.6650 (mpt180) REVERT: D 516 SER cc_start: 0.9503 (m) cc_final: 0.9018 (p) REVERT: D 640 MET cc_start: 0.7964 (mtp) cc_final: 0.7494 (mtm) REVERT: F 452 ASN cc_start: 0.8554 (m110) cc_final: 0.8084 (m110) REVERT: F 682 GLU cc_start: 0.4697 (pm20) cc_final: 0.3934 (pm20) REVERT: L 81 ASP cc_start: 0.8711 (t0) cc_final: 0.8486 (t0) REVERT: L 82 ARG cc_start: 0.8759 (ptt-90) cc_final: 0.8541 (ptt90) REVERT: L 126 GLU cc_start: 0.8964 (mp0) cc_final: 0.8511 (mp0) outliers start: 31 outliers final: 19 residues processed: 205 average time/residue: 0.9957 time to fit residues: 226.3160 Evaluate side-chains 206 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 494 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 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 H residue 43 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.078303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064775 restraints weight = 34407.851| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.91 r_work: 0.2974 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12439 Z= 0.138 Angle : 0.556 9.602 16915 Z= 0.280 Chirality : 0.042 0.237 1757 Planarity : 0.004 0.033 2227 Dihedral : 4.588 33.167 1660 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 12.94 % Favored : 84.70 % 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: -0.42 (0.21), residues: 1482 helix: -2.33 (0.60), residues: 72 sheet: 0.45 (0.31), residues: 237 loop : -0.29 (0.18), residues: 1173 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 0.012 0.001 PHE H 97 TYR 0.014 0.001 TYR C 484 ARG 0.004 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 249) hydrogen bonds : angle 5.13170 ( 597) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.08028 ( 4) covalent geometry : bond 0.00320 (12437) covalent geometry : angle 0.55601 (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 227 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.404 Fit side-chains REVERT: A 488 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.5827 (mmt180) REVERT: A 626 ASP cc_start: 0.8500 (m-30) cc_final: 0.8196 (m-30) REVERT: A 649 ILE cc_start: 0.5467 (OUTLIER) cc_final: 0.4973 (tp) REVERT: C 514 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7606 (tmt-80) REVERT: C 516 SER cc_start: 0.8627 (m) cc_final: 0.8094 (p) REVERT: C 532 ASP cc_start: 0.8368 (m-30) cc_final: 0.8141 (p0) REVERT: C 592 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: D 361 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8120 (pp20) REVERT: D 398 GLU cc_start: 0.4565 (tm-30) cc_final: 0.4205 (tm-30) REVERT: D 488 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.6555 (mmt180) REVERT: D 516 SER cc_start: 0.9470 (m) cc_final: 0.8991 (p) REVERT: D 640 MET cc_start: 0.7926 (mtp) cc_final: 0.7463 (mtm) REVERT: F 452 ASN cc_start: 0.8527 (m110) cc_final: 0.8037 (m110) REVERT: F 682 GLU cc_start: 0.4564 (pm20) cc_final: 0.3908 (pm20) REVERT: H 127 ASP cc_start: 0.8634 (m-30) cc_final: 0.8425 (m-30) REVERT: L 81 ASP cc_start: 0.8752 (t0) cc_final: 0.8517 (t0) REVERT: L 104 GLU cc_start: 0.9040 (tt0) cc_final: 0.8642 (tp30) REVERT: L 126 GLU cc_start: 0.8966 (mp0) cc_final: 0.8388 (mp0) outliers start: 31 outliers final: 19 residues processed: 208 average time/residue: 0.9753 time to fit residues: 225.1033 Evaluate side-chains 201 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 VAL 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 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 45 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 110 optimal weight: 0.0670 chunk 128 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 2.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 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 = 0.3380 r_free = 0.3380 target = 0.079002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065493 restraints weight = 34031.923| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.91 r_work: 0.2992 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12439 Z= 0.116 Angle : 0.554 9.394 16915 Z= 0.278 Chirality : 0.042 0.235 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.397 33.274 1660 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.13 % Allowed : 13.93 % Favored : 83.94 % 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: -0.35 (0.21), residues: 1482 helix: -2.15 (0.69), residues: 60 sheet: 0.30 (0.30), residues: 257 loop : -0.23 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 509 HIS 0.005 0.001 HIS H 69 PHE 0.014 0.001 PHE A 662 TYR 0.013 0.001 TYR C 484 ARG 0.005 0.000 ARG L 124 Details of bonding type rmsd hydrogen bonds : bond 0.02537 ( 249) hydrogen bonds : angle 4.96920 ( 597) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.98166 ( 4) covalent geometry : bond 0.00269 (12437) covalent geometry : angle 0.55361 (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 218 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.453 Fit side-chains REVERT: A 488 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.5805 (mmt180) REVERT: A 626 ASP cc_start: 0.8483 (m-30) cc_final: 0.8193 (m-30) REVERT: A 649 ILE cc_start: 0.5459 (OUTLIER) cc_final: 0.4961 (tp) REVERT: C 514 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7615 (tmt-80) REVERT: C 516 SER cc_start: 0.8638 (m) cc_final: 0.8082 (p) REVERT: C 532 ASP cc_start: 0.8351 (m-30) cc_final: 0.8141 (p0) REVERT: C 592 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: D 361 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8130 (pp20) REVERT: D 398 GLU cc_start: 0.4681 (tm-30) cc_final: 0.4304 (tm-30) REVERT: D 488 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.6902 (mmt180) REVERT: D 516 SER cc_start: 0.9482 (m) cc_final: 0.8999 (p) REVERT: D 640 MET cc_start: 0.7915 (mtp) cc_final: 0.7445 (mtm) REVERT: F 452 ASN cc_start: 0.8534 (m110) cc_final: 0.8046 (m110) REVERT: F 584 HIS cc_start: 0.8660 (m170) cc_final: 0.7931 (t70) REVERT: F 682 GLU cc_start: 0.4445 (pm20) cc_final: 0.3843 (pm20) REVERT: H 97 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7735 (t80) REVERT: H 127 ASP cc_start: 0.8659 (m-30) cc_final: 0.8450 (m-30) REVERT: L 81 ASP cc_start: 0.8758 (t0) cc_final: 0.8503 (t0) REVERT: L 103 ASP cc_start: 0.8749 (m-30) cc_final: 0.8533 (m-30) REVERT: L 104 GLU cc_start: 0.9018 (tt0) cc_final: 0.8642 (tp30) REVERT: L 126 GLU cc_start: 0.8972 (mp0) cc_final: 0.8523 (mp0) outliers start: 28 outliers final: 17 residues processed: 205 average time/residue: 1.0237 time to fit residues: 231.9765 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 459 GLN 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 D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 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 L residue 45 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 0.0980 chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066311 restraints weight = 34056.365| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.94 r_work: 0.3010 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12439 Z= 0.101 Angle : 0.560 9.929 16915 Z= 0.279 Chirality : 0.041 0.235 1757 Planarity : 0.004 0.034 2227 Dihedral : 4.224 31.452 1660 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 14.69 % Favored : 83.56 % 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: -2.20 (0.66), residues: 66 sheet: 0.43 (0.30), 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 0.013 0.001 PHE H 97 TYR 0.013 0.001 TYR C 484 ARG 0.003 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.02474 ( 249) hydrogen bonds : angle 4.83934 ( 597) SS BOND : bond 0.00242 ( 2) SS BOND : angle 1.01761 ( 4) covalent geometry : bond 0.00237 (12437) covalent geometry : angle 0.55951 (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 221 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.8920 (m-30) cc_final: 0.8410 (m-30) REVERT: A 488 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.5829 (mmt180) REVERT: A 626 ASP cc_start: 0.8489 (m-30) cc_final: 0.8189 (m-30) REVERT: A 649 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5050 (tp) REVERT: C 514 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7613 (tmt-80) REVERT: C 516 SER cc_start: 0.8649 (m) cc_final: 0.8070 (p) REVERT: C 532 ASP cc_start: 0.8327 (m-30) cc_final: 0.8124 (p0) REVERT: C 592 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: D 361 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8124 (pp20) REVERT: D 398 GLU cc_start: 0.4722 (tm-30) cc_final: 0.4341 (tm-30) REVERT: D 486 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8670 (mt0) REVERT: D 488 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.6923 (mmt180) REVERT: D 516 SER cc_start: 0.9487 (m) cc_final: 0.9008 (p) REVERT: F 452 ASN cc_start: 0.8546 (m110) cc_final: 0.8052 (m110) REVERT: F 584 HIS cc_start: 0.8646 (m170) cc_final: 0.7929 (t70) REVERT: F 682 GLU cc_start: 0.4360 (pm20) cc_final: 0.3780 (pm20) REVERT: H 62 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8792 (mttp) REVERT: H 97 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7790 (t80) REVERT: L 124 ARG cc_start: 0.9244 (ttm170) cc_final: 0.8987 (tmm160) REVERT: L 126 GLU cc_start: 0.8913 (mp0) cc_final: 0.8541 (mp0) outliers start: 23 outliers final: 13 residues processed: 215 average time/residue: 0.9510 time to fit residues: 227.5700 Evaluate side-chains 204 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 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 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 74 optimal weight: 40.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 L 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.078669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065066 restraints weight = 33989.444| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.89 r_work: 0.2986 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12439 Z= 0.155 Angle : 0.575 9.604 16915 Z= 0.289 Chirality : 0.042 0.229 1757 Planarity : 0.004 0.035 2227 Dihedral : 4.276 19.499 1659 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.60 % Allowed : 15.30 % Favored : 83.11 % 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: -2.11 (0.69), residues: 60 sheet: 0.43 (0.31), residues: 257 loop : -0.22 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 509 HIS 0.007 0.001 HIS H 69 PHE 0.014 0.001 PHE H 97 TYR 0.015 0.001 TYR C 484 ARG 0.003 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02597 ( 249) hydrogen bonds : angle 4.97340 ( 597) SS BOND : bond 0.00251 ( 2) SS BOND : angle 1.02245 ( 4) covalent geometry : bond 0.00360 (12437) covalent geometry : angle 0.57526 (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 207 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.287 Fit side-chains REVERT: A 488 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.5812 (mmt180) REVERT: A 626 ASP cc_start: 0.8497 (m-30) cc_final: 0.8200 (m-30) REVERT: A 649 ILE cc_start: 0.5446 (OUTLIER) cc_final: 0.4923 (tp) REVERT: C 514 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7637 (tmt-80) REVERT: C 516 SER cc_start: 0.8646 (m) cc_final: 0.8100 (p) REVERT: D 361 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8131 (pp20) REVERT: D 488 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.6924 (mmt180) REVERT: D 516 SER cc_start: 0.9501 (m) cc_final: 0.9052 (p) REVERT: F 452 ASN cc_start: 0.8529 (m110) cc_final: 0.8032 (m110) REVERT: F 584 HIS cc_start: 0.8685 (m170) cc_final: 0.7905 (t70) REVERT: F 682 GLU cc_start: 0.4518 (pm20) cc_final: 0.3939 (pm20) REVERT: H 127 ASP cc_start: 0.8555 (m-30) cc_final: 0.8207 (m-30) REVERT: L 104 GLU cc_start: 0.8973 (tt0) cc_final: 0.8625 (tp30) REVERT: L 126 GLU cc_start: 0.8834 (mp0) cc_final: 0.8348 (mp0) outliers start: 21 outliers final: 17 residues processed: 200 average time/residue: 0.9257 time to fit residues: 205.8897 Evaluate side-chains 200 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 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 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 496 ASN C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064948 restraints weight = 33983.489| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.90 r_work: 0.2982 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12439 Z= 0.163 Angle : 0.594 10.120 16915 Z= 0.300 Chirality : 0.042 0.224 1757 Planarity : 0.004 0.037 2227 Dihedral : 4.332 19.792 1659 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.67 % Allowed : 15.60 % Favored : 82.72 % 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: -0.35 (0.21), residues: 1482 helix: -2.21 (0.67), residues: 66 sheet: 0.37 (0.31), residues: 257 loop : -0.23 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 595 HIS 0.007 0.001 HIS H 69 PHE 0.013 0.001 PHE H 97 TYR 0.017 0.001 TYR H 72 ARG 0.003 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 249) hydrogen bonds : angle 5.02875 ( 597) SS BOND : bond 0.00223 ( 2) SS BOND : angle 1.09073 ( 4) covalent geometry : bond 0.00380 (12437) covalent geometry : angle 0.59355 (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 206 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.282 Fit side-chains REVERT: A 262 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8644 (p0) REVERT: A 488 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.5818 (mmt180) REVERT: A 601 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7381 (mp) REVERT: A 626 ASP cc_start: 0.8492 (m-30) cc_final: 0.8219 (m-30) REVERT: A 649 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.4896 (tp) REVERT: C 514 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7658 (mmt180) REVERT: C 516 SER cc_start: 0.8677 (m) cc_final: 0.8151 (p) REVERT: D 361 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8092 (pp20) REVERT: D 398 GLU cc_start: 0.5124 (tm-30) cc_final: 0.4755 (tm-30) REVERT: D 488 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.6598 (mpt180) REVERT: D 516 SER cc_start: 0.9521 (m) cc_final: 0.9077 (p) REVERT: D 518 MET cc_start: 0.8909 (tpp) cc_final: 0.8695 (ttp) REVERT: F 452 ASN cc_start: 0.8515 (m110) cc_final: 0.8015 (m110) REVERT: F 682 GLU cc_start: 0.4455 (pm20) cc_final: 0.3797 (pm20) REVERT: H 62 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8972 (tppp) REVERT: H 127 ASP cc_start: 0.8569 (m-30) cc_final: 0.8217 (m-30) REVERT: L 104 GLU cc_start: 0.8992 (tt0) cc_final: 0.8649 (tp30) REVERT: L 124 ARG cc_start: 0.9194 (tmm160) cc_final: 0.8760 (tmm-80) REVERT: L 126 GLU cc_start: 0.8856 (mp0) cc_final: 0.8435 (mp0) outliers start: 22 outliers final: 18 residues processed: 200 average time/residue: 0.9571 time to fit residues: 212.5657 Evaluate side-chains 202 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 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 45 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 19 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065000 restraints weight = 33901.923| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.88 r_work: 0.2984 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 12439 Z= 0.175 Angle : 0.829 59.043 16915 Z= 0.479 Chirality : 0.048 1.034 1757 Planarity : 0.004 0.037 2227 Dihedral : 4.385 28.121 1659 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.90 % Allowed : 15.22 % Favored : 82.88 % 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: -0.35 (0.21), residues: 1482 helix: -2.21 (0.67), residues: 66 sheet: 0.38 (0.31), residues: 257 loop : -0.23 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 595 HIS 0.006 0.001 HIS H 69 PHE 0.012 0.001 PHE H 97 TYR 0.015 0.001 TYR C 484 ARG 0.003 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.02630 ( 249) hydrogen bonds : angle 5.04105 ( 597) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.12689 ( 4) covalent geometry : bond 0.00390 (12437) covalent geometry : angle 0.82878 (16911) =============================================================================== Job complete usr+sys time: 9126.39 seconds wall clock time: 157 minutes 0.77 seconds (9420.77 seconds total)