Starting phenix.real_space_refine on Thu Aug 6 03:54:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.cif Found real_map, /net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.map" model { file = "/net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24id_69539/08_2026/24id_69539.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 82 5.16 5 C 8271 2.51 5 N 2211 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12928 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2255 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 11 Chain: "A" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7735 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 13 Chain: "B" Number of atoms: 2938 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2929 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 21, 'TRANS': 351} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 373, 2929 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 21, 'TRANS': 351} Chain breaks: 4 bond proxies already assigned to first conformer: 2984 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU B 612 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 612 " occ=0.50 Time building chain proxies: 3.02, per 1000 atoms: 0.23 Number of scatterers: 12928 At special positions: 0 Unit cell: (101.588, 109.044, 181.74, 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 82 16.00 O 2364 8.00 N 2211 7.00 C 8271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 605.2 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 33.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 86 through 99 removed outlier: 4.109A pdb=" N SER C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 165 removed outlier: 3.552A pdb=" N PHE C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.237A pdb=" N LEU C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 258 through 272 removed outlier: 4.321A pdb=" N THR C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 311 through 340 removed outlier: 3.698A pdb=" N PHE C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.878A pdb=" N LEU C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 374 through 394 removed outlier: 3.831A pdb=" N ASP C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.755A pdb=" N LYS A 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 908 through 921 removed outlier: 3.511A pdb=" N ARG A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 938 Processing helix chain 'A' and resid 1030 through 1039 Processing helix chain 'A' and resid 1049 through 1060 Processing helix chain 'A' and resid 1064 through 1073 Processing helix chain 'A' and resid 1081 through 1086 removed outlier: 3.681A pdb=" N TYR A1086 " --> pdb=" O TYR A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1101 through 1116 Processing helix chain 'A' and resid 1125 through 1135 Processing helix chain 'A' and resid 1136 through 1147 Processing helix chain 'A' and resid 1149 through 1164 Processing helix chain 'A' and resid 1172 through 1190 Processing helix chain 'A' and resid 1192 through 1204 removed outlier: 3.621A pdb=" N ALA A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.989A pdb=" N THR B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 4.175A pdb=" N LYS B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.716A pdb=" N PHE B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.777A pdb=" N LYS B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 595 removed outlier: 4.132A pdb=" N MET B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 removed outlier: 3.727A pdb=" N LEU B 625 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 733 through 748 Processing helix chain 'B' and resid 751 through 776 removed outlier: 3.643A pdb=" N PHE B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.532A pdb=" N ASN C 109 " --> pdb=" O TYR C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.551A pdb=" N LYS A 808 " --> pdb=" O CYS A 804 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 800 " --> pdb=" O ALA A 812 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.700A pdb=" N ASP A 47 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR A 53 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 69 removed outlier: 6.914A pdb=" N ALA A 89 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 67 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 87 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP A 69 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG A 85 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 90 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS A 107 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP A 99 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA A 105 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.870A pdb=" N ASP A 118 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.725A pdb=" N LEU A 177 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A 164 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 175 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'A' and resid 291 through 296 removed outlier: 3.556A pdb=" N ARG A 315 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 312 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN A 346 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 314 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 363 removed outlier: 4.148A pdb=" N SER A 360 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 374 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 458 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU A 384 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU A 456 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS A 386 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE A 454 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.512A pdb=" N ILE A 413 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 472 removed outlier: 6.336A pdb=" N HIS A 501 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 507 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 518 through 525 removed outlier: 3.947A pdb=" N GLY A 520 " --> pdb=" O PHE A 532 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 571 through 576 removed outlier: 3.550A pdb=" N GLU A 593 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 594 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 601 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 615 through 618 removed outlier: 3.858A pdb=" N ALA A 615 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 681 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 688 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG A 703 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N HIS A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 697 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 754 through 757 removed outlier: 3.721A pdb=" N LYS A 754 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 773 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.182A pdb=" N ILE B 378 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 477 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE B 380 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG B 377 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 500 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 580 through 583 removed outlier: 6.580A pdb=" N ARG B 569 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 612 through 617 removed outlier: 6.716A pdb=" N TYR B 655 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 725 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR B 657 " --> pdb=" O LEU B 723 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4177 1.35 - 1.46: 2938 1.46 - 1.58: 5961 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 13193 Sorted by residual: bond pdb=" C PRO A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.355 -0.022 2.34e-02 1.83e+03 8.48e-01 bond pdb=" CB PRO A 137 " pdb=" CG PRO A 137 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.72e-01 bond pdb=" CA ILE A 704 " pdb=" CB ILE A 704 " ideal model delta sigma weight residual 1.526 1.538 -0.012 1.55e-02 4.16e+03 6.42e-01 bond pdb=" C PHE B 618 " pdb=" N PRO B 619 " ideal model delta sigma weight residual 1.334 1.351 -0.018 2.34e-02 1.83e+03 5.60e-01 bond pdb=" CB PRO C 205 " pdb=" CG PRO C 205 " ideal model delta sigma weight residual 1.492 1.527 -0.035 5.00e-02 4.00e+02 4.93e-01 ... (remaining 13188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 17738 1.89 - 3.77: 111 3.77 - 5.66: 6 5.66 - 7.55: 2 7.55 - 9.43: 2 Bond angle restraints: 17859 Sorted by residual: angle pdb=" CA LEU A 271 " pdb=" CB LEU A 271 " pdb=" CG LEU A 271 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.26e+00 angle pdb=" N ARG C 294 " pdb=" CA ARG C 294 " pdb=" C ARG C 294 " ideal model delta sigma weight residual 114.04 110.82 3.22 1.24e+00 6.50e-01 6.74e+00 angle pdb=" CA LEU A 303 " pdb=" CB LEU A 303 " pdb=" CG LEU A 303 " ideal model delta sigma weight residual 116.30 124.98 -8.68 3.50e+00 8.16e-02 6.15e+00 angle pdb=" N PRO A 138 " pdb=" CA PRO A 138 " pdb=" C PRO A 138 " ideal model delta sigma weight residual 112.47 116.55 -4.08 2.06e+00 2.36e-01 3.93e+00 angle pdb=" C ALA A 146 " pdb=" N ASP A 147 " pdb=" CA ASP A 147 " ideal model delta sigma weight residual 121.54 124.89 -3.35 1.91e+00 2.74e-01 3.07e+00 ... (remaining 17854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7610 17.12 - 34.24: 271 34.24 - 51.36: 33 51.36 - 68.48: 4 68.48 - 85.60: 1 Dihedral angle restraints: 7919 sinusoidal: 3173 harmonic: 4746 Sorted by residual: dihedral pdb=" CA PRO A 137 " pdb=" C PRO A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta harmonic sigma weight residual -180.00 -163.92 -16.08 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU C 163 " pdb=" CG GLU C 163 " pdb=" CD GLU C 163 " pdb=" OE1 GLU C 163 " ideal model delta sinusoidal sigma weight residual 0.00 85.60 -85.60 1 3.00e+01 1.11e-03 9.85e+00 dihedral pdb=" N LEU A 870 " pdb=" CA LEU A 870 " pdb=" CB LEU A 870 " pdb=" CG LEU A 870 " ideal model delta sinusoidal sigma weight residual 180.00 -122.74 -57.26 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 7916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1343 0.030 - 0.060: 493 0.060 - 0.091: 110 0.091 - 0.121: 92 0.121 - 0.151: 8 Chirality restraints: 2046 Sorted by residual: chirality pdb=" CG LEU A 271 " pdb=" CB LEU A 271 " pdb=" CD1 LEU A 271 " pdb=" CD2 LEU A 271 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA PRO A 138 " pdb=" N PRO A 138 " pdb=" C PRO A 138 " pdb=" CB PRO A 138 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB ILE A 141 " pdb=" CA ILE A 141 " pdb=" CG1 ILE A 141 " pdb=" CG2 ILE A 141 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 2043 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 136 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 137 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 463 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 464 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 518 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 519 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.017 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3347 2.81 - 3.33: 11621 3.33 - 3.85: 20861 3.85 - 4.38: 23942 4.38 - 4.90: 42044 Nonbonded interactions: 101815 Sorted by model distance: nonbonded pdb=" OG1 THR A 614 " pdb=" O THR A 682 " model vdw 2.282 3.040 nonbonded pdb=" O LYS C 240 " pdb=" ND2 ASN C 244 " model vdw 2.305 3.120 nonbonded pdb=" ND2 ASN A 258 " pdb=" OE2 GLU A 274 " model vdw 2.315 3.120 nonbonded pdb=" OH TYR C 125 " pdb=" OD1 ASP C 170 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASN A 20 " pdb=" NE2 HIS A 40 " model vdw 2.320 3.120 ... (remaining 101810 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 10.890 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 : 0.002 0.044 13194 Z= 0.076 Angle : 0.397 9.432 17861 Z= 0.215 Chirality : 0.038 0.151 2046 Planarity : 0.003 0.042 2252 Dihedral : 8.442 85.603 4820 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.99 % Allowed : 4.10 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.18), residues: 1575 helix: 0.17 (0.21), residues: 510 sheet: -2.36 (0.26), residues: 323 loop : -3.02 (0.18), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 315 TYR 0.005 0.001 TYR A 140 PHE 0.007 0.001 PHE B 618 TRP 0.007 0.001 TRP A 751 HIS 0.002 0.000 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.08 (13193) covalent geometry : angle 0.39725 / 0.21 (17859) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.43278 / 0.23 ( 2) hydrogen bonds : bond 0.16972 / 11.19 ( 515) hydrogen bonds : angle 6.80986 / 4.81 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 199 PHE cc_start: 0.6332 (t80) cc_final: 0.6104 (t80) REVERT: C 200 GLU cc_start: 0.7041 (tt0) cc_final: 0.6754 (tt0) REVERT: C 322 PHE cc_start: 0.7743 (t80) cc_final: 0.7407 (t80) REVERT: C 323 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7652 (mtmt) REVERT: C 334 LYS cc_start: 0.6372 (mtpp) cc_final: 0.6142 (mtpp) REVERT: C 363 LEU cc_start: 0.7777 (mt) cc_final: 0.7576 (mp) REVERT: C 385 GLU cc_start: 0.6799 (tt0) cc_final: 0.6509 (tt0) REVERT: C 387 PHE cc_start: 0.7851 (t80) cc_final: 0.7591 (t80) REVERT: A 86 LEU cc_start: 0.7917 (tt) cc_final: 0.7619 (tt) REVERT: A 91 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8418 (t) REVERT: A 119 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 164 PHE cc_start: 0.7308 (p90) cc_final: 0.6761 (p90) REVERT: A 192 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8574 (ttmm) REVERT: A 279 VAL cc_start: 0.7711 (m) cc_final: 0.7443 (p) REVERT: A 340 THR cc_start: 0.7590 (m) cc_final: 0.7098 (p) REVERT: A 351 ARG cc_start: 0.6704 (ttm110) cc_final: 0.6390 (ttm110) REVERT: A 353 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 568 GLU cc_start: 0.7606 (tt0) cc_final: 0.7057 (tt0) REVERT: A 575 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7665 (mmtp) REVERT: A 579 LEU cc_start: 0.8492 (mp) cc_final: 0.8232 (mm) REVERT: A 682 THR cc_start: 0.7368 (m) cc_final: 0.7124 (p) REVERT: A 687 GLN cc_start: 0.7065 (tp40) cc_final: 0.6620 (tp-100) REVERT: A 688 VAL cc_start: 0.8075 (t) cc_final: 0.7806 (t) REVERT: A 689 TYR cc_start: 0.7116 (m-80) cc_final: 0.6672 (m-80) REVERT: A 765 LYS cc_start: 0.7682 (mptt) cc_final: 0.7107 (mptt) REVERT: A 783 GLN cc_start: 0.7045 (mt0) cc_final: 0.6770 (mt0) REVERT: A 841 VAL cc_start: 0.8205 (t) cc_final: 0.7797 (p) REVERT: A 900 LYS cc_start: 0.7313 (mttt) cc_final: 0.6893 (mttt) REVERT: A 907 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6620 (t80) REVERT: A 1057 MET cc_start: 0.5218 (mtp) cc_final: 0.4720 (mtp) REVERT: A 1147 MET cc_start: 0.6700 (mtp) cc_final: 0.6492 (mtp) REVERT: A 1148 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7232 (ttm110) REVERT: B 375 THR cc_start: 0.8673 (m) cc_final: 0.8394 (p) REVERT: B 447 ASN cc_start: 0.7701 (m110) cc_final: 0.7376 (m-40) REVERT: B 496 LYS cc_start: 0.7824 (mttt) cc_final: 0.7550 (mttt) REVERT: B 582 VAL cc_start: 0.7872 (t) cc_final: 0.7601 (m) REVERT: B 738 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6869 (ttp-110) outliers start: 43 outliers final: 19 residues processed: 403 average time/residue: 0.1158 time to fit residues: 65.6565 Evaluate side-chains 334 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 253 GLN C 301 GLN C 371 HIS C 394 GLN A 23 ASN A 110 GLN A 117 GLN A 120 GLN A 125 GLN A 433 GLN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 581 GLN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 HIS ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 861 HIS A 867 GLN A 888 GLN A 961 ASN A1068 GLN A1084 GLN A1090 ASN A1145 HIS B 455 ASN B 461 GLN B 464 GLN B 495 ASN B 577 HIS B 586 ASN B 641 GLN B 645 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141960 restraints weight = 33203.018| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.62 r_work: 0.3574 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 13194 Z= 0.247 Angle : 0.610 10.407 17861 Z= 0.305 Chirality : 0.045 0.185 2046 Planarity : 0.005 0.058 2252 Dihedral : 5.659 56.404 1778 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.68 % Allowed : 11.46 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.21), residues: 1575 helix: 1.04 (0.22), residues: 515 sheet: -1.74 (0.27), residues: 356 loop : -2.43 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.026 0.002 TYR C 227 PHE 0.034 0.002 PHE A 679 TRP 0.020 0.002 TRP A 144 HIS 0.008 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (13193) covalent geometry : angle 0.60969 / 0.30 (17859) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 2.44116 / 1.30 ( 2) hydrogen bonds : bond 0.03922 / 2.61 ( 515) hydrogen bonds : angle 5.17748 / 3.68 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7063 (mm-30) REVERT: C 261 MET cc_start: -0.0463 (mmt) cc_final: -0.0702 (mmt) REVERT: C 334 LYS cc_start: 0.6643 (mtpp) cc_final: 0.6379 (mtpp) REVERT: C 385 GLU cc_start: 0.7194 (tt0) cc_final: 0.6840 (tt0) REVERT: C 387 PHE cc_start: 0.7963 (t80) cc_final: 0.7673 (t80) REVERT: C 390 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6350 (mm-30) REVERT: A 24 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8186 (mtmm) REVERT: A 86 LEU cc_start: 0.8235 (tt) cc_final: 0.7942 (tt) REVERT: A 144 TRP cc_start: 0.8359 (m100) cc_final: 0.8027 (m100) REVERT: A 154 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8261 (ttmm) REVERT: A 155 LYS cc_start: 0.8738 (tptm) cc_final: 0.8374 (tptm) REVERT: A 266 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8063 (mtp85) REVERT: A 272 ASP cc_start: 0.7170 (t0) cc_final: 0.6783 (t0) REVERT: A 279 VAL cc_start: 0.7970 (m) cc_final: 0.7739 (p) REVERT: A 282 ILE cc_start: 0.8351 (mm) cc_final: 0.8141 (mt) REVERT: A 340 THR cc_start: 0.7962 (m) cc_final: 0.7473 (p) REVERT: A 351 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7436 (ttm110) REVERT: A 386 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7683 (mmmm) REVERT: A 422 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 496 SER cc_start: 0.8175 (m) cc_final: 0.7692 (p) REVERT: A 568 GLU cc_start: 0.8153 (tt0) cc_final: 0.7714 (tt0) REVERT: A 575 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8114 (mmtp) REVERT: A 579 LEU cc_start: 0.8616 (mp) cc_final: 0.8309 (mt) REVERT: A 582 TYR cc_start: 0.8216 (m-80) cc_final: 0.7990 (m-80) REVERT: A 687 GLN cc_start: 0.7754 (tp40) cc_final: 0.7203 (tp-100) REVERT: A 689 TYR cc_start: 0.7400 (m-80) cc_final: 0.6997 (m-80) REVERT: A 724 VAL cc_start: 0.8640 (t) cc_final: 0.8397 (m) REVERT: A 731 ASN cc_start: 0.7966 (m-40) cc_final: 0.7743 (m-40) REVERT: A 743 ARG cc_start: 0.7954 (mpp80) cc_final: 0.7670 (mpp80) REVERT: A 745 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 783 GLN cc_start: 0.7925 (mt0) cc_final: 0.7520 (mt0) REVERT: A 784 MET cc_start: 0.7957 (ttm) cc_final: 0.7674 (ttm) REVERT: A 826 LYS cc_start: 0.8596 (mttt) cc_final: 0.8130 (mtmm) REVERT: A 841 VAL cc_start: 0.8216 (t) cc_final: 0.7893 (p) REVERT: A 900 LYS cc_start: 0.7568 (mttt) cc_final: 0.7134 (mttt) REVERT: A 907 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 937 HIS cc_start: 0.7713 (t-90) cc_final: 0.7271 (t-90) REVERT: A 1057 MET cc_start: 0.5259 (mtp) cc_final: 0.4758 (mtp) REVERT: A 1148 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7764 (ttm110) REVERT: B 375 THR cc_start: 0.8663 (m) cc_final: 0.8369 (p) REVERT: B 400 LYS cc_start: 0.7790 (mppt) cc_final: 0.7570 (mmtm) REVERT: B 446 ARG cc_start: 0.7966 (ptm-80) cc_final: 0.7685 (ptm160) REVERT: B 476 LEU cc_start: 0.8524 (mt) cc_final: 0.8273 (mp) REVERT: B 486 ASP cc_start: 0.8297 (m-30) cc_final: 0.8065 (m-30) REVERT: B 558 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7457 (mtp85) REVERT: B 641 GLN cc_start: 0.8294 (mm110) cc_final: 0.8022 (mm110) REVERT: B 663 SER cc_start: 0.8652 (t) cc_final: 0.8442 (t) REVERT: B 738 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7381 (ttp-110) outliers start: 53 outliers final: 33 residues processed: 367 average time/residue: 0.1172 time to fit residues: 60.2685 Evaluate side-chains 351 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 48 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 289 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 HIS ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 447 ASN B 495 ASN B 586 ASN B 641 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140501 restraints weight = 34421.585| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.72 r_work: 0.3540 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13194 Z= 0.223 Angle : 0.596 10.144 17861 Z= 0.295 Chirality : 0.044 0.179 2046 Planarity : 0.005 0.055 2252 Dihedral : 5.422 59.097 1761 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.17 % Allowed : 13.12 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1575 helix: 1.39 (0.23), residues: 516 sheet: -1.39 (0.27), residues: 368 loop : -2.27 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.021 0.002 TYR C 227 PHE 0.031 0.002 PHE A 679 TRP 0.024 0.002 TRP A 735 HIS 0.009 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (13193) covalent geometry : angle 0.59557 / 0.30 (17859) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 1.87489 / 1.00 ( 2) hydrogen bonds : bond 0.03478 / 2.29 ( 515) hydrogen bonds : angle 4.91979 / 3.51 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 163 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7203 (mm-30) REVERT: C 323 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7918 (mtmt) REVERT: C 334 LYS cc_start: 0.6639 (mtpp) cc_final: 0.6370 (mtpp) REVERT: C 385 GLU cc_start: 0.7244 (tt0) cc_final: 0.6876 (tt0) REVERT: C 387 PHE cc_start: 0.7952 (t80) cc_final: 0.7728 (t80) REVERT: C 390 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6340 (mm-30) REVERT: A 24 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8147 (mtmm) REVERT: A 86 LEU cc_start: 0.8229 (tt) cc_final: 0.7929 (tt) REVERT: A 154 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8264 (ttmm) REVERT: A 155 LYS cc_start: 0.8693 (tptm) cc_final: 0.8461 (tptt) REVERT: A 272 ASP cc_start: 0.7285 (t0) cc_final: 0.6936 (t0) REVERT: A 279 VAL cc_start: 0.8103 (m) cc_final: 0.7868 (p) REVERT: A 317 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7259 (tmm-80) REVERT: A 340 THR cc_start: 0.7887 (m) cc_final: 0.7472 (p) REVERT: A 351 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7495 (ttm110) REVERT: A 360 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8429 (m) REVERT: A 386 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7689 (mmmm) REVERT: A 422 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 496 SER cc_start: 0.8184 (m) cc_final: 0.7704 (p) REVERT: A 522 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6800 (mt-10) REVERT: A 579 LEU cc_start: 0.8693 (mp) cc_final: 0.8415 (mt) REVERT: A 582 TYR cc_start: 0.8045 (m-80) cc_final: 0.7749 (m-80) REVERT: A 687 GLN cc_start: 0.7730 (tp40) cc_final: 0.7320 (tp-100) REVERT: A 724 VAL cc_start: 0.8613 (t) cc_final: 0.8378 (m) REVERT: A 743 ARG cc_start: 0.7979 (mpp80) cc_final: 0.7724 (mpp80) REVERT: A 772 ASP cc_start: 0.7805 (p0) cc_final: 0.7559 (p0) REVERT: A 783 GLN cc_start: 0.7953 (mt0) cc_final: 0.7543 (mt0) REVERT: A 826 LYS cc_start: 0.8658 (mttt) cc_final: 0.8218 (mtmm) REVERT: A 841 VAL cc_start: 0.8142 (t) cc_final: 0.7784 (p) REVERT: A 900 LYS cc_start: 0.7573 (mttt) cc_final: 0.7141 (mttt) REVERT: A 907 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 937 HIS cc_start: 0.7804 (t-90) cc_final: 0.7377 (t-90) REVERT: A 1057 MET cc_start: 0.5333 (mtp) cc_final: 0.4808 (mtp) REVERT: A 1148 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7790 (ttm110) REVERT: B 375 THR cc_start: 0.8647 (m) cc_final: 0.8362 (p) REVERT: B 392 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7747 (ttp) REVERT: B 476 LEU cc_start: 0.8435 (mt) cc_final: 0.8220 (mp) REVERT: B 551 LEU cc_start: 0.8022 (mt) cc_final: 0.7807 (mt) REVERT: B 641 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7713 (mm-40) REVERT: B 738 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7399 (ttp-110) outliers start: 60 outliers final: 41 residues processed: 359 average time/residue: 0.1122 time to fit residues: 57.1452 Evaluate side-chains 360 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 139 optimal weight: 0.0000 chunk 71 optimal weight: 0.3980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A1145 HIS B 455 ASN B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.176364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141330 restraints weight = 34680.137| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.75 r_work: 0.3557 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13194 Z= 0.167 Angle : 0.562 9.984 17861 Z= 0.277 Chirality : 0.043 0.169 2046 Planarity : 0.004 0.064 2252 Dihedral : 5.380 59.888 1761 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.68 % Allowed : 15.49 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1575 helix: 1.64 (0.23), residues: 519 sheet: -1.25 (0.28), residues: 370 loop : -2.08 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.027 0.001 TYR C 227 PHE 0.027 0.002 PHE A 679 TRP 0.033 0.002 TRP A 735 HIS 0.007 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (13193) covalent geometry : angle 0.56226 / 0.28 (17859) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 1.43005 / 0.76 ( 2) hydrogen bonds : bond 0.03110 / 2.03 ( 515) hydrogen bonds : angle 4.70029 / 3.34 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 316 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 295 PHE cc_start: 0.7586 (t80) cc_final: 0.7337 (t80) REVERT: C 323 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7908 (mtmt) REVERT: C 334 LYS cc_start: 0.6630 (mtpp) cc_final: 0.6370 (mtpp) REVERT: C 390 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6317 (mm-30) REVERT: A 24 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8107 (mtmm) REVERT: A 86 LEU cc_start: 0.8220 (tt) cc_final: 0.7922 (tt) REVERT: A 118 ASP cc_start: 0.7640 (t0) cc_final: 0.7064 (m-30) REVERT: A 119 VAL cc_start: 0.8085 (p) cc_final: 0.7005 (m) REVERT: A 154 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8204 (ttmm) REVERT: A 279 VAL cc_start: 0.8155 (m) cc_final: 0.7916 (p) REVERT: A 317 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7200 (tmm-80) REVERT: A 340 THR cc_start: 0.7880 (m) cc_final: 0.7446 (p) REVERT: A 351 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7494 (ttm110) REVERT: A 360 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8446 (m) REVERT: A 386 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7554 (mmmm) REVERT: A 422 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7506 (mt) REVERT: A 496 SER cc_start: 0.8166 (m) cc_final: 0.7683 (p) REVERT: A 522 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6786 (mt-10) REVERT: A 579 LEU cc_start: 0.8670 (mp) cc_final: 0.8353 (mt) REVERT: A 582 TYR cc_start: 0.8016 (m-80) cc_final: 0.7653 (m-80) REVERT: A 687 GLN cc_start: 0.7701 (tp40) cc_final: 0.7228 (tp-100) REVERT: A 724 VAL cc_start: 0.8620 (t) cc_final: 0.8364 (m) REVERT: A 743 ARG cc_start: 0.7986 (mpp80) cc_final: 0.7722 (mpp80) REVERT: A 772 ASP cc_start: 0.7751 (p0) cc_final: 0.7475 (p0) REVERT: A 783 GLN cc_start: 0.7926 (mt0) cc_final: 0.7515 (mt0) REVERT: A 826 LYS cc_start: 0.8607 (mttt) cc_final: 0.8152 (mtmm) REVERT: A 900 LYS cc_start: 0.7574 (mttt) cc_final: 0.7171 (mttt) REVERT: A 907 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7052 (t80) REVERT: A 937 HIS cc_start: 0.7817 (t-90) cc_final: 0.7365 (t-90) REVERT: A 1057 MET cc_start: 0.5340 (mtp) cc_final: 0.4811 (mtp) REVERT: A 1148 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7798 (ttm110) REVERT: A 1173 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6868 (tp30) REVERT: B 375 THR cc_start: 0.8619 (m) cc_final: 0.8345 (p) REVERT: B 389 PHE cc_start: 0.8418 (m-80) cc_final: 0.7741 (m-80) REVERT: B 392 MET cc_start: 0.7959 (ttp) cc_final: 0.7682 (ttp) REVERT: B 738 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7382 (ttp-110) outliers start: 53 outliers final: 38 residues processed: 349 average time/residue: 0.1234 time to fit residues: 59.9598 Evaluate side-chains 350 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 47 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.174247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138296 restraints weight = 40793.621| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.15 r_work: 0.3498 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13194 Z= 0.262 Angle : 0.618 10.675 17861 Z= 0.307 Chirality : 0.045 0.183 2046 Planarity : 0.005 0.079 2252 Dihedral : 5.419 57.063 1759 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.51 % Allowed : 15.76 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.22), residues: 1575 helix: 1.64 (0.23), residues: 517 sheet: -1.17 (0.28), residues: 372 loop : -2.03 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.026 0.002 TYR C 227 PHE 0.027 0.003 PHE B 772 TRP 0.020 0.002 TRP A 735 HIS 0.009 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (13193) covalent geometry : angle 0.61787 / 0.31 (17859) SS BOND : bond 0.01038 / 0.55 ( 1) SS BOND : angle 1.25485 / 0.69 ( 2) hydrogen bonds : bond 0.03466 / 2.26 ( 515) hydrogen bonds : angle 4.82074 / 3.43 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 320 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: C 163 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 295 PHE cc_start: 0.7517 (t80) cc_final: 0.7248 (t80) REVERT: C 323 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7933 (mtmt) REVERT: C 334 LYS cc_start: 0.6668 (mtpp) cc_final: 0.6401 (mtpp) REVERT: C 387 PHE cc_start: 0.8092 (t80) cc_final: 0.7883 (t80) REVERT: C 390 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6367 (mm-30) REVERT: A 24 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8115 (mtmm) REVERT: A 86 LEU cc_start: 0.8288 (tt) cc_final: 0.7977 (tt) REVERT: A 118 ASP cc_start: 0.7715 (t0) cc_final: 0.7080 (m-30) REVERT: A 154 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8336 (ttmm) REVERT: A 259 HIS cc_start: 0.7300 (m-70) cc_final: 0.7082 (m-70) REVERT: A 279 VAL cc_start: 0.8276 (m) cc_final: 0.8052 (p) REVERT: A 317 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7232 (tmm-80) REVERT: A 340 THR cc_start: 0.7975 (m) cc_final: 0.7530 (p) REVERT: A 351 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7559 (ttm110) REVERT: A 360 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (m) REVERT: A 386 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7743 (mmmm) REVERT: A 422 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7427 (mt) REVERT: A 496 SER cc_start: 0.8250 (m) cc_final: 0.7785 (p) REVERT: A 522 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6981 (mt-10) REVERT: A 579 LEU cc_start: 0.8721 (mp) cc_final: 0.8390 (mm) REVERT: A 608 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8457 (tptm) REVERT: A 687 GLN cc_start: 0.7766 (tp40) cc_final: 0.7305 (tp-100) REVERT: A 689 TYR cc_start: 0.7732 (m-80) cc_final: 0.7459 (m-80) REVERT: A 724 VAL cc_start: 0.8653 (t) cc_final: 0.8361 (m) REVERT: A 745 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7536 (tp) REVERT: A 772 ASP cc_start: 0.7746 (p0) cc_final: 0.7465 (p0) REVERT: A 775 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7511 (mm-30) REVERT: A 783 GLN cc_start: 0.8010 (mt0) cc_final: 0.7621 (mt0) REVERT: A 826 LYS cc_start: 0.8638 (mttt) cc_final: 0.8190 (mtmm) REVERT: A 887 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 900 LYS cc_start: 0.7640 (mttt) cc_final: 0.7264 (mttt) REVERT: A 907 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 929 TRP cc_start: 0.8141 (m100) cc_final: 0.7938 (m100) REVERT: A 937 HIS cc_start: 0.7907 (t-90) cc_final: 0.7442 (t-90) REVERT: A 1057 MET cc_start: 0.5374 (mtp) cc_final: 0.4838 (mtp) REVERT: A 1148 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7870 (ttm110) REVERT: A 1173 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7198 (tp30) REVERT: B 375 THR cc_start: 0.8654 (m) cc_final: 0.8360 (p) REVERT: B 389 PHE cc_start: 0.8434 (m-80) cc_final: 0.7785 (m-80) REVERT: B 392 MET cc_start: 0.8072 (ttp) cc_final: 0.7781 (ttp) REVERT: B 641 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 738 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7467 (ttp-110) outliers start: 65 outliers final: 48 residues processed: 356 average time/residue: 0.1028 time to fit residues: 51.4705 Evaluate side-chains 365 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 140 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.174184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139629 restraints weight = 32919.989| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.58 r_work: 0.3551 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13194 Z= 0.217 Angle : 0.597 10.492 17861 Z= 0.295 Chirality : 0.044 0.177 2046 Planarity : 0.005 0.065 2252 Dihedral : 5.244 53.286 1757 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.31 % Allowed : 16.81 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1575 helix: 1.77 (0.23), residues: 518 sheet: -1.12 (0.28), residues: 372 loop : -1.94 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.023 0.002 TYR C 227 PHE 0.029 0.002 PHE B 772 TRP 0.018 0.002 TRP A 735 HIS 0.007 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (13193) covalent geometry : angle 0.59701 / 0.30 (17859) SS BOND : bond 0.00401 / 0.21 ( 1) SS BOND : angle 1.80286 / 0.95 ( 2) hydrogen bonds : bond 0.03317 / 2.16 ( 515) hydrogen bonds : angle 4.72799 / 3.36 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: C 163 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: C 295 PHE cc_start: 0.7508 (t80) cc_final: 0.7271 (t80) REVERT: C 322 PHE cc_start: 0.8258 (t80) cc_final: 0.7847 (t80) REVERT: C 323 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7873 (mtmt) REVERT: C 334 LYS cc_start: 0.6612 (mtpp) cc_final: 0.6364 (mtpp) REVERT: C 387 PHE cc_start: 0.8064 (t80) cc_final: 0.7835 (t80) REVERT: C 390 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6389 (mm-30) REVERT: A 24 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8084 (mtmm) REVERT: A 86 LEU cc_start: 0.8281 (tt) cc_final: 0.7971 (tt) REVERT: A 118 ASP cc_start: 0.7716 (t0) cc_final: 0.7019 (m-30) REVERT: A 154 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8225 (ttmm) REVERT: A 272 ASP cc_start: 0.7105 (t0) cc_final: 0.6847 (t0) REVERT: A 279 VAL cc_start: 0.8282 (m) cc_final: 0.8065 (p) REVERT: A 300 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7827 (mmt90) REVERT: A 317 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.7240 (tmm-80) REVERT: A 340 THR cc_start: 0.7942 (m) cc_final: 0.7491 (p) REVERT: A 351 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7387 (ttm110) REVERT: A 360 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (m) REVERT: A 386 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7581 (mmmm) REVERT: A 422 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7389 (mt) REVERT: A 496 SER cc_start: 0.8199 (m) cc_final: 0.7585 (p) REVERT: A 522 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6757 (mt-10) REVERT: A 579 LEU cc_start: 0.8718 (mp) cc_final: 0.8388 (mm) REVERT: A 608 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8461 (tptm) REVERT: A 617 GLU cc_start: 0.7856 (tp30) cc_final: 0.7594 (tp30) REVERT: A 676 ARG cc_start: 0.7309 (tpp80) cc_final: 0.6993 (tpp80) REVERT: A 687 GLN cc_start: 0.7677 (tp40) cc_final: 0.7224 (tp-100) REVERT: A 689 TYR cc_start: 0.7648 (m-80) cc_final: 0.7425 (m-80) REVERT: A 724 VAL cc_start: 0.8574 (t) cc_final: 0.8288 (m) REVERT: A 745 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7527 (tp) REVERT: A 765 LYS cc_start: 0.8044 (mptt) cc_final: 0.7453 (mptt) REVERT: A 775 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7509 (mm-30) REVERT: A 782 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7912 (t) REVERT: A 783 GLN cc_start: 0.7897 (mt0) cc_final: 0.7534 (mt0) REVERT: A 789 ARG cc_start: 0.7800 (tpt170) cc_final: 0.7275 (tpt170) REVERT: A 826 LYS cc_start: 0.8633 (mttt) cc_final: 0.8176 (mtmm) REVERT: A 887 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6973 (tp) REVERT: A 900 LYS cc_start: 0.7636 (mttt) cc_final: 0.7254 (mttt) REVERT: A 907 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 937 HIS cc_start: 0.7772 (t-90) cc_final: 0.7292 (t-90) REVERT: A 1057 MET cc_start: 0.5394 (mtp) cc_final: 0.4863 (mtp) REVERT: A 1147 MET cc_start: 0.7784 (mtp) cc_final: 0.7552 (mtp) REVERT: A 1148 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7813 (ttm110) REVERT: A 1173 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7203 (tp30) REVERT: B 375 THR cc_start: 0.8703 (m) cc_final: 0.8396 (p) REVERT: B 377 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8449 (mtp85) REVERT: B 389 PHE cc_start: 0.8409 (m-80) cc_final: 0.7855 (m-80) REVERT: B 641 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7678 (mm-40) REVERT: B 738 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7381 (ttp-110) outliers start: 62 outliers final: 46 residues processed: 346 average time/residue: 0.1188 time to fit residues: 57.8756 Evaluate side-chains 363 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 816 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139564 restraints weight = 38982.204| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 4.04 r_work: 0.3529 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13194 Z= 0.195 Angle : 0.585 11.039 17861 Z= 0.289 Chirality : 0.043 0.174 2046 Planarity : 0.004 0.058 2252 Dihedral : 5.207 53.136 1757 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.65 % Allowed : 16.74 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1575 helix: 1.86 (0.23), residues: 519 sheet: -1.07 (0.28), residues: 372 loop : -1.85 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.020 0.002 TYR C 227 PHE 0.031 0.002 PHE B 772 TRP 0.019 0.002 TRP A 735 HIS 0.007 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (13193) covalent geometry : angle 0.58470 / 0.29 (17859) SS BOND : bond 0.00252 / 0.13 ( 1) SS BOND : angle 1.79883 / 0.96 ( 2) hydrogen bonds : bond 0.03188 / 2.08 ( 515) hydrogen bonds : angle 4.62139 / 3.28 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 295 PHE cc_start: 0.7473 (t80) cc_final: 0.7223 (t80) REVERT: C 323 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7925 (mtmt) REVERT: C 334 LYS cc_start: 0.6625 (mtpp) cc_final: 0.6361 (mtpp) REVERT: C 387 PHE cc_start: 0.8062 (t80) cc_final: 0.7803 (t80) REVERT: C 390 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6411 (mm-30) REVERT: A 24 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8097 (mtmm) REVERT: A 86 LEU cc_start: 0.8286 (tt) cc_final: 0.7977 (tt) REVERT: A 118 ASP cc_start: 0.7759 (t0) cc_final: 0.7010 (m-30) REVERT: A 154 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8265 (ttmm) REVERT: A 155 LYS cc_start: 0.8704 (tptt) cc_final: 0.8388 (tptm) REVERT: A 272 ASP cc_start: 0.7066 (t0) cc_final: 0.6728 (t0) REVERT: A 279 VAL cc_start: 0.8305 (m) cc_final: 0.8091 (p) REVERT: A 317 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7166 (ttt-90) REVERT: A 340 THR cc_start: 0.7929 (m) cc_final: 0.7484 (p) REVERT: A 351 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7412 (ttm110) REVERT: A 360 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 386 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7755 (mmmm) REVERT: A 422 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7289 (mt) REVERT: A 496 SER cc_start: 0.8136 (m) cc_final: 0.7570 (p) REVERT: A 522 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6885 (mt-10) REVERT: A 579 LEU cc_start: 0.8721 (mp) cc_final: 0.8401 (mm) REVERT: A 608 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8462 (tptm) REVERT: A 617 GLU cc_start: 0.7867 (tp30) cc_final: 0.7603 (tp30) REVERT: A 619 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8219 (t) REVERT: A 687 GLN cc_start: 0.7706 (tp40) cc_final: 0.7251 (tp-100) REVERT: A 689 TYR cc_start: 0.7669 (m-80) cc_final: 0.7451 (m-80) REVERT: A 724 VAL cc_start: 0.8625 (t) cc_final: 0.8360 (m) REVERT: A 765 LYS cc_start: 0.8062 (mptt) cc_final: 0.7450 (mptt) REVERT: A 775 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 782 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 783 GLN cc_start: 0.7837 (mt0) cc_final: 0.7457 (mt0) REVERT: A 784 MET cc_start: 0.7531 (tpp) cc_final: 0.7202 (tpt) REVERT: A 789 ARG cc_start: 0.7847 (tpt170) cc_final: 0.7275 (tpt170) REVERT: A 826 LYS cc_start: 0.8634 (mttt) cc_final: 0.8166 (mtmm) REVERT: A 887 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6984 (tp) REVERT: A 900 LYS cc_start: 0.7654 (mttt) cc_final: 0.7272 (mttt) REVERT: A 907 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7069 (t80) REVERT: A 937 HIS cc_start: 0.7826 (t-90) cc_final: 0.7346 (t-90) REVERT: A 1057 MET cc_start: 0.5377 (mtp) cc_final: 0.4848 (mtp) REVERT: A 1147 MET cc_start: 0.7844 (mtp) cc_final: 0.7613 (mtp) REVERT: A 1148 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7854 (ttm110) REVERT: A 1173 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 375 THR cc_start: 0.8713 (m) cc_final: 0.8396 (p) REVERT: B 377 ARG cc_start: 0.8713 (mtp85) cc_final: 0.8486 (mtp85) REVERT: B 389 PHE cc_start: 0.8418 (m-80) cc_final: 0.7856 (m-80) REVERT: B 392 MET cc_start: 0.8113 (ttp) cc_final: 0.7896 (ttp) REVERT: B 400 LYS cc_start: 0.7879 (mppt) cc_final: 0.7635 (mmtm) REVERT: B 641 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7697 (mm-40) REVERT: B 738 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7444 (ttp-110) outliers start: 67 outliers final: 47 residues processed: 357 average time/residue: 0.1207 time to fit residues: 61.0553 Evaluate side-chains 365 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 815 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 136 optimal weight: 0.4980 chunk 139 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141447 restraints weight = 27460.300| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.22 r_work: 0.3593 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13194 Z= 0.170 Angle : 0.583 11.495 17861 Z= 0.285 Chirality : 0.043 0.169 2046 Planarity : 0.004 0.050 2252 Dihedral : 5.141 53.672 1755 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.17 % Allowed : 17.43 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1575 helix: 1.98 (0.23), residues: 517 sheet: -1.01 (0.28), residues: 367 loop : -1.84 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.019 0.001 TYR A 252 PHE 0.033 0.002 PHE B 772 TRP 0.019 0.002 TRP A 735 HIS 0.006 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13193) covalent geometry : angle 0.58300 / 0.29 (17859) SS BOND : bond 0.00234 / 0.12 ( 1) SS BOND : angle 1.77651 / 0.95 ( 2) hydrogen bonds : bond 0.03074 / 2.01 ( 515) hydrogen bonds : angle 4.53241 / 3.22 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 295 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 334 LYS cc_start: 0.6568 (mtpp) cc_final: 0.6316 (mtpp) REVERT: C 387 PHE cc_start: 0.7991 (t80) cc_final: 0.7744 (t80) REVERT: C 390 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6414 (mm-30) REVERT: A 24 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8061 (mtmm) REVERT: A 86 LEU cc_start: 0.8255 (tt) cc_final: 0.7941 (tt) REVERT: A 118 ASP cc_start: 0.7707 (t0) cc_final: 0.6981 (m-30) REVERT: A 154 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8170 (ttmm) REVERT: A 157 TYR cc_start: 0.7267 (m-80) cc_final: 0.6953 (m-80) REVERT: A 279 VAL cc_start: 0.8234 (m) cc_final: 0.8020 (p) REVERT: A 317 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7078 (ttt-90) REVERT: A 340 THR cc_start: 0.7879 (m) cc_final: 0.7438 (p) REVERT: A 351 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7252 (ttm110) REVERT: A 360 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8414 (m) REVERT: A 386 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7699 (mmmm) REVERT: A 422 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7301 (mt) REVERT: A 522 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6743 (mt-10) REVERT: A 579 LEU cc_start: 0.8701 (mp) cc_final: 0.8420 (mm) REVERT: A 608 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (tptm) REVERT: A 617 GLU cc_start: 0.7693 (tp30) cc_final: 0.7419 (tp30) REVERT: A 687 GLN cc_start: 0.7625 (tp40) cc_final: 0.7117 (tp-100) REVERT: A 724 VAL cc_start: 0.8558 (t) cc_final: 0.8288 (m) REVERT: A 745 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7556 (tp) REVERT: A 765 LYS cc_start: 0.8021 (mptt) cc_final: 0.7493 (mptt) REVERT: A 775 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 782 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7902 (t) REVERT: A 783 GLN cc_start: 0.7795 (mt0) cc_final: 0.7408 (mt0) REVERT: A 784 MET cc_start: 0.7457 (tpp) cc_final: 0.6964 (tpt) REVERT: A 826 LYS cc_start: 0.8615 (mttt) cc_final: 0.8147 (mtmm) REVERT: A 887 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6939 (tp) REVERT: A 900 LYS cc_start: 0.7705 (mttt) cc_final: 0.7327 (mttt) REVERT: A 907 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 937 HIS cc_start: 0.7720 (t-90) cc_final: 0.7241 (t-90) REVERT: A 1057 MET cc_start: 0.5359 (mtp) cc_final: 0.4835 (mtp) REVERT: A 1147 MET cc_start: 0.7734 (mtp) cc_final: 0.7514 (mtp) REVERT: A 1148 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7820 (ttm110) REVERT: A 1173 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 1188 LYS cc_start: 0.7738 (tttm) cc_final: 0.7377 (tttm) REVERT: B 375 THR cc_start: 0.8595 (m) cc_final: 0.8272 (p) REVERT: B 389 PHE cc_start: 0.8389 (m-80) cc_final: 0.7820 (m-80) REVERT: B 392 MET cc_start: 0.8055 (ttp) cc_final: 0.7838 (ttp) REVERT: B 641 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7636 (mm-40) REVERT: B 738 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7350 (ttp-110) outliers start: 60 outliers final: 42 residues processed: 345 average time/residue: 0.1236 time to fit residues: 60.2033 Evaluate side-chains 357 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 815 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 110 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 105 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140739 restraints weight = 31025.476| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.47 r_work: 0.3580 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13194 Z= 0.189 Angle : 0.594 11.626 17861 Z= 0.292 Chirality : 0.044 0.171 2046 Planarity : 0.004 0.053 2252 Dihedral : 5.147 53.906 1755 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.03 % Allowed : 17.99 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1575 helix: 2.01 (0.23), residues: 517 sheet: -0.98 (0.29), residues: 366 loop : -1.80 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.020 0.002 TYR A 252 PHE 0.034 0.002 PHE B 772 TRP 0.017 0.002 TRP A 735 HIS 0.007 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (13193) covalent geometry : angle 0.59326 / 0.29 (17859) SS BOND : bond 0.00207 / 0.11 ( 1) SS BOND : angle 1.77863 / 0.95 ( 2) hydrogen bonds : bond 0.03145 / 2.06 ( 515) hydrogen bonds : angle 4.54647 / 3.23 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 334 LYS cc_start: 0.6595 (mtpp) cc_final: 0.6333 (mtpp) REVERT: C 387 PHE cc_start: 0.8020 (t80) cc_final: 0.7776 (t80) REVERT: C 390 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6420 (mm-30) REVERT: A 24 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8076 (mtmm) REVERT: A 86 LEU cc_start: 0.8270 (tt) cc_final: 0.7959 (tt) REVERT: A 118 ASP cc_start: 0.7732 (t0) cc_final: 0.7073 (m-30) REVERT: A 154 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8220 (ttmm) REVERT: A 279 VAL cc_start: 0.8286 (m) cc_final: 0.8070 (p) REVERT: A 340 THR cc_start: 0.7904 (m) cc_final: 0.7453 (p) REVERT: A 351 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7351 (ttm110) REVERT: A 360 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8455 (m) REVERT: A 386 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7673 (mmmm) REVERT: A 422 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 507 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 522 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6804 (mt-10) REVERT: A 579 LEU cc_start: 0.8743 (mp) cc_final: 0.8404 (mt) REVERT: A 608 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8459 (tptm) REVERT: A 617 GLU cc_start: 0.7779 (tp30) cc_final: 0.7531 (tp30) REVERT: A 687 GLN cc_start: 0.7681 (tp40) cc_final: 0.7218 (tp-100) REVERT: A 724 VAL cc_start: 0.8583 (t) cc_final: 0.8308 (m) REVERT: A 745 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7633 (tp) REVERT: A 764 GLN cc_start: 0.7983 (mm110) cc_final: 0.7241 (mp-120) REVERT: A 765 LYS cc_start: 0.8022 (mptt) cc_final: 0.7504 (mptt) REVERT: A 782 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7921 (t) REVERT: A 783 GLN cc_start: 0.7874 (mt0) cc_final: 0.7486 (mt0) REVERT: A 784 MET cc_start: 0.7529 (tpp) cc_final: 0.7309 (tpt) REVERT: A 826 LYS cc_start: 0.8611 (mttt) cc_final: 0.8176 (mtmm) REVERT: A 887 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6971 (tp) REVERT: A 900 LYS cc_start: 0.7705 (mttt) cc_final: 0.7334 (mttt) REVERT: A 907 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 937 HIS cc_start: 0.7743 (t-90) cc_final: 0.7265 (t-90) REVERT: A 1057 MET cc_start: 0.5335 (mtp) cc_final: 0.4838 (mtp) REVERT: A 1147 MET cc_start: 0.7770 (mtp) cc_final: 0.7548 (mtp) REVERT: A 1148 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7849 (ttm110) REVERT: A 1173 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 1188 LYS cc_start: 0.7742 (tttm) cc_final: 0.7381 (tttm) REVERT: B 375 THR cc_start: 0.8587 (m) cc_final: 0.8270 (p) REVERT: B 377 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8229 (mtp85) REVERT: B 392 MET cc_start: 0.8030 (ttp) cc_final: 0.7815 (ttp) REVERT: B 641 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7661 (mm-40) REVERT: B 738 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: B 772 PHE cc_start: 0.7822 (t80) cc_final: 0.7464 (t80) outliers start: 58 outliers final: 43 residues processed: 337 average time/residue: 0.1322 time to fit residues: 62.7878 Evaluate side-chains 357 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 815 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 5.9990 chunk 144 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 152 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 HIS B 495 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.175224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138532 restraints weight = 44691.005| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.41 r_work: 0.3491 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13194 Z= 0.210 Angle : 0.606 11.058 17861 Z= 0.300 Chirality : 0.044 0.174 2046 Planarity : 0.004 0.055 2252 Dihedral : 5.209 53.160 1755 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.82 % Allowed : 18.12 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.22), residues: 1575 helix: 1.96 (0.23), residues: 517 sheet: -0.94 (0.29), residues: 361 loop : -1.81 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.018 0.002 TYR A 341 PHE 0.033 0.002 PHE B 772 TRP 0.024 0.002 TRP C 299 HIS 0.008 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (13193) covalent geometry : angle 0.60582 / 0.30 (17859) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 1.77067 / 0.95 ( 2) hydrogen bonds : bond 0.03299 / 2.17 ( 515) hydrogen bonds : angle 4.59861 / 3.26 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4513 (tp) REVERT: C 322 PHE cc_start: 0.8321 (t80) cc_final: 0.8107 (t80) REVERT: C 334 LYS cc_start: 0.6609 (mtpp) cc_final: 0.6348 (mtpp) REVERT: C 387 PHE cc_start: 0.8062 (t80) cc_final: 0.7793 (t80) REVERT: C 390 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6435 (mm-30) REVERT: A 24 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8094 (mtmm) REVERT: A 86 LEU cc_start: 0.8291 (tt) cc_final: 0.7985 (tt) REVERT: A 154 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8366 (ttmm) REVERT: A 155 LYS cc_start: 0.8761 (tptt) cc_final: 0.8440 (tptm) REVERT: A 279 VAL cc_start: 0.8358 (m) cc_final: 0.8150 (p) REVERT: A 340 THR cc_start: 0.7994 (m) cc_final: 0.7518 (p) REVERT: A 341 TYR cc_start: 0.8447 (m-80) cc_final: 0.8033 (m-80) REVERT: A 351 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7445 (ttm110) REVERT: A 360 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8496 (m) REVERT: A 386 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7750 (mmmm) REVERT: A 422 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7308 (mt) REVERT: A 496 SER cc_start: 0.8195 (m) cc_final: 0.7688 (p) REVERT: A 507 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 522 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6953 (mt-10) REVERT: A 579 LEU cc_start: 0.8753 (mp) cc_final: 0.8411 (mt) REVERT: A 608 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (tptm) REVERT: A 617 GLU cc_start: 0.7920 (tp30) cc_final: 0.7651 (tp30) REVERT: A 687 GLN cc_start: 0.7771 (tp40) cc_final: 0.7289 (tp-100) REVERT: A 745 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (tp) REVERT: A 765 LYS cc_start: 0.8037 (mptt) cc_final: 0.7523 (mptt) REVERT: A 782 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7944 (t) REVERT: A 783 GLN cc_start: 0.7973 (mt0) cc_final: 0.7620 (mt0) REVERT: A 826 LYS cc_start: 0.8645 (mttt) cc_final: 0.8221 (mtmm) REVERT: A 887 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6974 (tp) REVERT: A 900 LYS cc_start: 0.7669 (mttt) cc_final: 0.7303 (mttt) REVERT: A 907 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 937 HIS cc_start: 0.7929 (t-90) cc_final: 0.7456 (t-90) REVERT: A 1057 MET cc_start: 0.5399 (mtp) cc_final: 0.4858 (mtp) REVERT: A 1147 MET cc_start: 0.7901 (mtp) cc_final: 0.7688 (mtp) REVERT: A 1148 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7928 (ttm110) REVERT: A 1173 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7203 (tm-30) REVERT: A 1188 LYS cc_start: 0.7780 (tttm) cc_final: 0.7413 (tttm) REVERT: B 375 THR cc_start: 0.8604 (m) cc_final: 0.8278 (p) REVERT: B 392 MET cc_start: 0.8134 (ttp) cc_final: 0.7917 (ttp) REVERT: B 641 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7725 (mm-40) REVERT: B 738 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7511 (ttp-110) outliers start: 55 outliers final: 43 residues processed: 332 average time/residue: 0.1334 time to fit residues: 62.3709 Evaluate side-chains 353 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1136 CYS Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 815 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 127 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 0.0470 chunk 120 optimal weight: 0.5980 chunk 118 optimal weight: 0.0870 chunk 141 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 623 ASN A1145 HIS B 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.176164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142566 restraints weight = 27416.278| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.22 r_work: 0.3600 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13194 Z= 0.130 Angle : 0.577 11.313 17861 Z= 0.282 Chirality : 0.043 0.168 2046 Planarity : 0.004 0.050 2252 Dihedral : 5.067 53.762 1755 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.33 % Allowed : 18.96 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1575 helix: 2.04 (0.23), residues: 517 sheet: -0.89 (0.28), residues: 366 loop : -1.69 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.019 0.001 TYR C 227 PHE 0.033 0.002 PHE B 772 TRP 0.023 0.002 TRP C 299 HIS 0.005 0.001 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13193) covalent geometry : angle 0.57651 / 0.28 (17859) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 1.72449 / 0.93 ( 2) hydrogen bonds : bond 0.02973 / 1.95 ( 515) hydrogen bonds : angle 4.45298 / 3.15 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.06 seconds wall clock time: 62 minutes 55.25 seconds (3775.25 seconds total)