Starting phenix.real_space_refine on Tue Jun 17 17:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgs_36245/06_2025/8jgs_36245.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 6630 2.51 5 N 1650 2.21 5 O 1740 1.98 5 H 10182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10134 Classifications: {'peptide': 639} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Chain breaks: 6 Chain: "B" Number of atoms: 10134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10134 Classifications: {'peptide': 639} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Chain breaks: 6 Time building chain proxies: 15.91, per 1000 atoms: 0.78 Number of scatterers: 20268 At special positions: 0 Unit cell: (97.65, 99.51, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1740 8.00 N 1650 7.00 C 6630 6.00 H 10182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 498 " - pdb=" SG CYS B 504 " 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: 9.72 Conformation dependent library (CDL) restraints added in 4.9 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 69.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.751A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 91 removed outlier: 3.679A pdb=" N MET A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 143 through 169 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.048A pdb=" N LEU A 193 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 220 through 235 removed outlier: 4.040A pdb=" N LEU A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.541A pdb=" N LYS A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 282 through 302 removed outlier: 4.014A pdb=" N TRP A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.011A pdb=" N PHE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.754A pdb=" N ARG A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.514A pdb=" N GLY A 360 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 removed outlier: 3.558A pdb=" N ALA A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.836A pdb=" N PHE A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 489 removed outlier: 3.656A pdb=" N VAL A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.592A pdb=" N GLU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 removed outlier: 3.565A pdb=" N TYR A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.618A pdb=" N THR A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 removed outlier: 4.338A pdb=" N LEU A 546 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.200A pdb=" N VAL A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 703 through 714 removed outlier: 4.316A pdb=" N ASP A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 50 through 91 removed outlier: 3.838A pdb=" N MET B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 143 through 169 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.067A pdb=" N LEU B 193 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 220 through 235 removed outlier: 3.588A pdb=" N SER B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 242 through 261 removed outlier: 4.554A pdb=" N ALA B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.764A pdb=" N LEU B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.968A pdb=" N PHE B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.910A pdb=" N ARG B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 379 removed outlier: 3.820A pdb=" N PHE B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 433 through 452 Processing helix chain 'B' and resid 462 through 489 removed outlier: 3.747A pdb=" N VAL B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 506 through 524 removed outlier: 3.565A pdb=" N TYR B 510 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 removed outlier: 3.627A pdb=" N THR B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 559 removed outlier: 4.216A pdb=" N LEU B 546 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 559 " --> pdb=" O TRP B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 572 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 645 through 659 Processing helix chain 'B' and resid 703 through 714 removed outlier: 3.552A pdb=" N VAL B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 97 removed outlier: 3.898A pdb=" N ILE A 96 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 127 " --> pdb=" O ILE A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.692A pdb=" N PHE A 628 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.038A pdb=" N VAL A 698 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS A 719 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 730 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 721 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.791A pdb=" N ILE B 96 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 127 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 627 through 628 removed outlier: 3.674A pdb=" N PHE B 628 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 643 " --> pdb=" O PHE B 628 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 697 through 699 removed outlier: 6.132A pdb=" N VAL B 698 " --> pdb=" O THR B 722 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 719 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 730 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 721 " --> pdb=" O LEU B 728 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1746 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: 13.99 Time building geometry restraints manager: 10.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10160 1.03 - 1.23: 42 1.23 - 1.43: 4378 1.43 - 1.62: 5856 1.62 - 1.82: 98 Bond restraints: 20534 Sorted by residual: bond pdb=" CB TRP A 153 " pdb=" CG TRP A 153 " ideal model delta sigma weight residual 1.498 1.534 -0.036 3.10e-02 1.04e+03 1.39e+00 bond pdb=" CE3 TRP A 153 " pdb=" HE3 TRP A 153 " ideal model delta sigma weight residual 0.930 0.908 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C THR A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.331 1.344 -0.012 1.21e-02 6.83e+03 1.05e+00 bond pdb=" CG TRP A 153 " pdb=" CD2 TRP A 153 " ideal model delta sigma weight residual 1.433 1.451 -0.018 1.80e-02 3.09e+03 1.00e+00 bond pdb=" CB TRP B 153 " pdb=" CG TRP B 153 " ideal model delta sigma weight residual 1.498 1.528 -0.030 3.10e-02 1.04e+03 9.36e-01 ... (remaining 20529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 33898 1.00 - 2.01: 2956 2.01 - 3.01: 190 3.01 - 4.01: 53 4.01 - 5.01: 13 Bond angle restraints: 37110 Sorted by residual: angle pdb=" N GLY B 267 " pdb=" CA GLY B 267 " pdb=" C GLY B 267 " ideal model delta sigma weight residual 112.73 108.68 4.05 1.20e+00 6.94e-01 1.14e+01 angle pdb=" CB TRP A 153 " pdb=" CG TRP A 153 " pdb=" CD2 TRP A 153 " ideal model delta sigma weight residual 126.80 130.73 -3.93 1.40e+00 5.10e-01 7.88e+00 angle pdb=" C TRP B 286 " pdb=" CA TRP B 286 " pdb=" CB TRP B 286 " ideal model delta sigma weight residual 110.88 114.60 -3.72 1.57e+00 4.06e-01 5.61e+00 angle pdb=" CB TRP A 153 " pdb=" CG TRP A 153 " pdb=" CD1 TRP A 153 " ideal model delta sigma weight residual 126.90 123.37 3.53 1.50e+00 4.44e-01 5.53e+00 angle pdb=" N GLU A 541 " pdb=" CA GLU A 541 " pdb=" C GLU A 541 " ideal model delta sigma weight residual 113.61 110.21 3.40 1.50e+00 4.44e-01 5.14e+00 ... (remaining 37105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8678 17.98 - 35.96: 721 35.96 - 53.93: 171 53.93 - 71.91: 74 71.91 - 89.89: 14 Dihedral angle restraints: 9658 sinusoidal: 5080 harmonic: 4578 Sorted by residual: dihedral pdb=" CA GLU A 274 " pdb=" C GLU A 274 " pdb=" N GLU A 275 " pdb=" CA GLU A 275 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" N GLU B 275 " pdb=" CA GLU B 275 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU B 540 " pdb=" C LEU B 540 " pdb=" N GLU B 541 " pdb=" CA GLU B 541 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 9655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1331 0.050 - 0.099: 216 0.099 - 0.148: 36 0.148 - 0.198: 1 0.198 - 0.247: 2 Chirality restraints: 1586 Sorted by residual: chirality pdb=" CA TRP A 153 " pdb=" N TRP A 153 " pdb=" C TRP A 153 " pdb=" CB TRP A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TRP B 153 " pdb=" N TRP B 153 " pdb=" C TRP B 153 " pdb=" CB TRP B 153 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 458 " pdb=" N VAL A 458 " pdb=" C VAL A 458 " pdb=" CB VAL A 458 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1583 not shown) Planarity restraints: 2932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.029 2.00e-02 2.50e+03 1.95e-02 1.51e+01 pdb=" CG TRP B 286 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP B 286 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP B 286 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 286 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 286 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 286 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP B 286 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 153 " 0.016 2.00e-02 2.50e+03 1.44e-02 8.29e+00 pdb=" CG TRP A 153 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 153 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 153 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 153 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 153 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 153 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 153 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 153 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 153 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 153 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 153 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 153 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 153 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 157 " 0.013 2.00e-02 2.50e+03 1.20e-02 4.33e+00 pdb=" CG PHE A 157 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 157 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 157 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 157 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 157 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 157 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 157 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 157 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 157 " -0.001 2.00e-02 2.50e+03 ... (remaining 2929 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1378 2.19 - 2.80: 42512 2.80 - 3.40: 56531 3.40 - 4.00: 69336 4.00 - 4.60: 108710 Nonbonded interactions: 278467 Sorted by model distance: nonbonded pdb=" O GLY A 219 " pdb=" H VAL A 222 " model vdw 1.593 2.450 nonbonded pdb=" O MET A 449 " pdb=" HG1 THR A 453 " model vdw 1.597 2.450 nonbonded pdb=" O HIS B 25 " pdb=" H ILE B 188 " model vdw 1.609 2.450 nonbonded pdb=" H TYR A 322 " pdb=" OE2 GLU A 325 " model vdw 1.626 2.450 nonbonded pdb=" O MET B 449 " pdb=" HG1 THR B 453 " model vdw 1.637 2.450 ... (remaining 278462 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 273.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.460 Extract box with map and model: 1.020 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 81.970 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.130 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: 0.030 Load rotamer database and sin/cos tables:4.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4504 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 : 0.003 0.036 10358 Z= 0.148 Angle : 0.568 5.013 14062 Z= 0.334 Chirality : 0.038 0.247 1586 Planarity : 0.005 0.074 1718 Dihedral : 13.467 89.890 3632 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1250 helix: 0.02 (0.18), residues: 780 sheet: 1.16 (1.20), residues: 20 loop : -1.01 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 286 HIS 0.006 0.001 HIS A 223 PHE 0.035 0.002 PHE A 157 TYR 0.019 0.001 TYR B 59 ARG 0.013 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.16704 ( 590) hydrogen bonds : angle 6.95290 ( 1746) SS BOND : bond 0.00106 ( 6) SS BOND : angle 0.80803 ( 12) covalent geometry : bond 0.00299 (10352) covalent geometry : angle 0.56816 (14050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7450 (m) cc_final: 0.7233 (m) REVERT: A 449 MET cc_start: 0.1924 (tpp) cc_final: 0.1633 (tpp) REVERT: B 69 THR cc_start: 0.7698 (m) cc_final: 0.7430 (m) REVERT: B 457 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7232 (tttt) REVERT: B 693 MET cc_start: 0.6619 (mmm) cc_final: 0.6110 (mtp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.7138 time to fit residues: 155.5151 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.306207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.280170 restraints weight = 43872.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.287475 restraints weight = 24652.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.292299 restraints weight = 15696.488| |-----------------------------------------------------------------------------| r_work (final): 0.5002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4632 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10358 Z= 0.190 Angle : 0.611 6.018 14062 Z= 0.347 Chirality : 0.039 0.153 1586 Planarity : 0.005 0.050 1718 Dihedral : 4.824 24.609 1376 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.75 % Allowed : 7.24 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1250 helix: 0.35 (0.18), residues: 782 sheet: 0.70 (1.09), residues: 20 loop : -1.12 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 286 HIS 0.009 0.002 HIS B 569 PHE 0.029 0.002 PHE A 534 TYR 0.015 0.001 TYR B 278 ARG 0.006 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.05462 ( 590) hydrogen bonds : angle 5.41749 ( 1746) SS BOND : bond 0.00233 ( 6) SS BOND : angle 0.61048 ( 12) covalent geometry : bond 0.00396 (10352) covalent geometry : angle 0.61075 (14050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7416 (tttt) REVERT: B 693 MET cc_start: 0.6416 (mmm) cc_final: 0.5814 (mtp) outliers start: 8 outliers final: 6 residues processed: 148 average time/residue: 0.8571 time to fit residues: 186.8447 Evaluate side-chains 136 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.308058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.282630 restraints weight = 43943.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.289875 restraints weight = 24646.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.294661 restraints weight = 15675.692| |-----------------------------------------------------------------------------| r_work (final): 0.5019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4565 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10358 Z= 0.136 Angle : 0.539 7.025 14062 Z= 0.300 Chirality : 0.038 0.143 1586 Planarity : 0.004 0.046 1718 Dihedral : 4.580 24.353 1376 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.56 % Allowed : 8.74 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1250 helix: 0.71 (0.18), residues: 788 sheet: 0.32 (1.05), residues: 20 loop : -1.07 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 286 HIS 0.005 0.001 HIS A 739 PHE 0.033 0.002 PHE A 157 TYR 0.013 0.001 TYR B 147 ARG 0.005 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 590) hydrogen bonds : angle 5.10237 ( 1746) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.42589 ( 12) covalent geometry : bond 0.00286 (10352) covalent geometry : angle 0.53881 (14050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7331 (tttt) REVERT: B 693 MET cc_start: 0.6022 (mmm) cc_final: 0.5659 (mtp) outliers start: 6 outliers final: 6 residues processed: 147 average time/residue: 0.4906 time to fit residues: 102.5849 Evaluate side-chains 138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.305659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.279726 restraints weight = 44247.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.286852 restraints weight = 24809.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.291607 restraints weight = 15813.496| |-----------------------------------------------------------------------------| r_work (final): 0.4997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4650 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10358 Z= 0.155 Angle : 0.556 6.983 14062 Z= 0.310 Chirality : 0.038 0.147 1586 Planarity : 0.005 0.052 1718 Dihedral : 4.569 22.164 1376 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.13 % Allowed : 10.53 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1250 helix: 0.73 (0.18), residues: 776 sheet: 0.05 (1.04), residues: 20 loop : -0.96 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 286 HIS 0.006 0.001 HIS A 223 PHE 0.029 0.002 PHE A 157 TYR 0.012 0.001 TYR B 147 ARG 0.004 0.000 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 590) hydrogen bonds : angle 5.04643 ( 1746) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.46552 ( 12) covalent geometry : bond 0.00329 (10352) covalent geometry : angle 0.55653 (14050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 TYR cc_start: 0.3765 (m-80) cc_final: 0.2993 (m-10) REVERT: B 693 MET cc_start: 0.6016 (mmm) cc_final: 0.5654 (mtp) outliers start: 12 outliers final: 12 residues processed: 146 average time/residue: 0.5191 time to fit residues: 108.2926 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.305321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.278795 restraints weight = 44444.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.285669 restraints weight = 25118.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.290617 restraints weight = 16457.822| |-----------------------------------------------------------------------------| r_work (final): 0.4996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4763 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10358 Z= 0.180 Angle : 0.582 8.332 14062 Z= 0.325 Chirality : 0.038 0.145 1586 Planarity : 0.005 0.044 1718 Dihedral : 4.703 23.022 1376 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.88 % Allowed : 12.03 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1250 helix: 0.59 (0.18), residues: 778 sheet: 0.15 (1.11), residues: 20 loop : -1.15 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 286 HIS 0.006 0.001 HIS B 223 PHE 0.033 0.002 PHE A 534 TYR 0.016 0.001 TYR B 278 ARG 0.005 0.000 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 590) hydrogen bonds : angle 5.14239 ( 1746) SS BOND : bond 0.00356 ( 6) SS BOND : angle 0.53037 ( 12) covalent geometry : bond 0.00390 (10352) covalent geometry : angle 0.58201 (14050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6535 (mm-30) cc_final: 0.5687 (mm-30) REVERT: A 619 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5301 (ptt) REVERT: B 383 TYR cc_start: 0.3741 (m-80) cc_final: 0.2953 (m-10) REVERT: B 693 MET cc_start: 0.6020 (mmm) cc_final: 0.5660 (mtp) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 0.6162 time to fit residues: 141.2546 Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 274 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.309509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.282784 restraints weight = 44336.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.289855 restraints weight = 24509.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.295110 restraints weight = 15648.778| |-----------------------------------------------------------------------------| r_work (final): 0.5042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10358 Z= 0.137 Angle : 0.535 7.140 14062 Z= 0.296 Chirality : 0.037 0.144 1586 Planarity : 0.004 0.043 1718 Dihedral : 4.527 22.746 1376 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.13 % Allowed : 13.44 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1250 helix: 0.78 (0.18), residues: 790 sheet: 0.11 (1.12), residues: 20 loop : -1.20 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 286 HIS 0.006 0.001 HIS A 223 PHE 0.030 0.002 PHE A 157 TYR 0.016 0.001 TYR B 278 ARG 0.007 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 590) hydrogen bonds : angle 4.89671 ( 1746) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.41278 ( 12) covalent geometry : bond 0.00294 (10352) covalent geometry : angle 0.53480 (14050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6488 (mm-30) cc_final: 0.5713 (mm-30) REVERT: B 383 TYR cc_start: 0.3705 (m-80) cc_final: 0.2928 (m-10) REVERT: B 588 THR cc_start: 0.2706 (m) cc_final: 0.2491 (m) REVERT: B 693 MET cc_start: 0.5973 (mmm) cc_final: 0.5574 (mtp) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.5475 time to fit residues: 113.6527 Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 274 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.299128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.270755 restraints weight = 44415.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.277224 restraints weight = 25549.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.281925 restraints weight = 17172.524| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10358 Z= 0.299 Angle : 0.740 7.265 14062 Z= 0.424 Chirality : 0.043 0.227 1586 Planarity : 0.006 0.065 1718 Dihedral : 5.447 28.342 1376 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.26 % Allowed : 13.72 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1250 helix: -0.13 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 286 HIS 0.009 0.002 HIS A 223 PHE 0.041 0.003 PHE A 534 TYR 0.025 0.002 TYR B 278 ARG 0.005 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.05629 ( 590) hydrogen bonds : angle 5.82890 ( 1746) SS BOND : bond 0.00587 ( 6) SS BOND : angle 0.85334 ( 12) covalent geometry : bond 0.00649 (10352) covalent geometry : angle 0.73971 (14050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6847 (mm-30) cc_final: 0.5993 (mm-30) REVERT: A 740 MET cc_start: 0.6635 (ptp) cc_final: 0.6373 (ptp) REVERT: B 300 ARG cc_start: 0.5683 (ttt180) cc_final: 0.5248 (ttp-170) REVERT: B 383 TYR cc_start: 0.4075 (m-80) cc_final: 0.3110 (m-10) REVERT: B 693 MET cc_start: 0.6158 (mmm) cc_final: 0.5946 (mtp) REVERT: B 740 MET cc_start: 0.6319 (ptp) cc_final: 0.6074 (ptp) outliers start: 24 outliers final: 21 residues processed: 146 average time/residue: 0.5057 time to fit residues: 104.5764 Evaluate side-chains 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.304490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.277737 restraints weight = 44193.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.284613 restraints weight = 24311.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.289540 restraints weight = 15631.859| |-----------------------------------------------------------------------------| r_work (final): 0.4994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10358 Z= 0.147 Angle : 0.568 6.394 14062 Z= 0.316 Chirality : 0.038 0.153 1586 Planarity : 0.005 0.054 1718 Dihedral : 4.896 23.572 1376 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.32 % Allowed : 14.85 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1250 helix: 0.37 (0.18), residues: 788 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.006 0.001 HIS A 569 PHE 0.034 0.002 PHE A 157 TYR 0.018 0.001 TYR B 278 ARG 0.006 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 590) hydrogen bonds : angle 5.19873 ( 1746) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.53063 ( 12) covalent geometry : bond 0.00313 (10352) covalent geometry : angle 0.56824 (14050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6562 (mm-30) cc_final: 0.5784 (mm-30) REVERT: B 383 TYR cc_start: 0.4050 (m-80) cc_final: 0.3126 (m-10) REVERT: B 693 MET cc_start: 0.6172 (mmm) cc_final: 0.5967 (mtp) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 0.5116 time to fit residues: 108.8295 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 274 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.304186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.277335 restraints weight = 44416.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.284404 restraints weight = 24692.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.289349 restraints weight = 15899.385| |-----------------------------------------------------------------------------| r_work (final): 0.4991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4840 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10358 Z= 0.156 Angle : 0.566 6.270 14062 Z= 0.316 Chirality : 0.037 0.150 1586 Planarity : 0.005 0.057 1718 Dihedral : 4.753 21.769 1376 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.13 % Allowed : 15.32 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1250 helix: 0.49 (0.18), residues: 788 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.006 0.001 HIS A 223 PHE 0.032 0.002 PHE A 157 TYR 0.019 0.001 TYR B 278 ARG 0.008 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 590) hydrogen bonds : angle 5.11382 ( 1746) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.54743 ( 12) covalent geometry : bond 0.00337 (10352) covalent geometry : angle 0.56552 (14050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6719 (mm-30) cc_final: 0.5819 (mm-30) REVERT: B 693 MET cc_start: 0.6067 (mmm) cc_final: 0.5619 (mtp) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.5093 time to fit residues: 105.0548 Evaluate side-chains 148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 739 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.301426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.272705 restraints weight = 41508.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.280362 restraints weight = 22612.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.285663 restraints weight = 14372.768| |-----------------------------------------------------------------------------| r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4840 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10358 Z= 0.159 Angle : 0.560 5.903 14062 Z= 0.315 Chirality : 0.037 0.146 1586 Planarity : 0.005 0.065 1718 Dihedral : 4.746 22.194 1376 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.13 % Allowed : 15.32 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1250 helix: 0.50 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 286 HIS 0.006 0.001 HIS B 223 PHE 0.035 0.002 PHE A 157 TYR 0.019 0.001 TYR B 278 ARG 0.007 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 590) hydrogen bonds : angle 5.10872 ( 1746) SS BOND : bond 0.00569 ( 6) SS BOND : angle 0.54356 ( 12) covalent geometry : bond 0.00342 (10352) covalent geometry : angle 0.56043 (14050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 543 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6650 (mm-30) cc_final: 0.5800 (mm-30) REVERT: B 693 MET cc_start: 0.6105 (mmm) cc_final: 0.5648 (mtp) outliers start: 12 outliers final: 11 residues processed: 149 average time/residue: 0.5246 time to fit residues: 110.5413 Evaluate side-chains 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 739 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.303672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.275523 restraints weight = 42035.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.283260 restraints weight = 22634.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.288524 restraints weight = 14203.480| |-----------------------------------------------------------------------------| r_work (final): 0.4982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4764 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10358 Z= 0.129 Angle : 0.543 7.166 14062 Z= 0.301 Chirality : 0.037 0.144 1586 Planarity : 0.005 0.058 1718 Dihedral : 4.550 21.544 1376 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.03 % Allowed : 15.88 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1250 helix: 0.70 (0.18), residues: 790 sheet: 0.42 (1.21), residues: 20 loop : -1.40 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 286 HIS 0.005 0.001 HIS B 223 PHE 0.035 0.002 PHE A 157 TYR 0.016 0.001 TYR B 278 ARG 0.009 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 590) hydrogen bonds : angle 4.90971 ( 1746) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.45184 ( 12) covalent geometry : bond 0.00277 (10352) covalent geometry : angle 0.54340 (14050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.03 seconds wall clock time: 133 minutes 14.74 seconds (7994.74 seconds total)