Starting phenix.real_space_refine on Tue May 20 15:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgs_36245/05_2025/8jgs_36245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgs_36245/05_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_36245/05_2025/8jgs_36245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgs_36245/05_2025/8jgs_36245.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgs_36245/05_2025/8jgs_36245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgs_36245/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.99, per 1000 atoms: 0.44 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: 4.90 Conformation dependent library (CDL) restraints added in 1.4 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: 1.55 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: 7.10 Time building geometry restraints manager: 5.93 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: 0.06 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- 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 : 1.503 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: 0.5102 time to fit residues: 107.1750 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 : 1.369 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.280231 restraints weight = 43872.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.287399 restraints weight = 24573.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.292309 restraints weight = 15710.677| |-----------------------------------------------------------------------------| 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 6.017 14062 Z= 0.347 Chirality : 0.039 0.153 1586 Planarity : 0.005 0.050 1718 Dihedral : 4.824 24.608 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 0.61041 ( 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 : 1.394 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: 0.6417 (mmm) cc_final: 0.5815 (mtp) outliers start: 8 outliers final: 6 residues processed: 148 average time/residue: 0.4703 time to fit residues: 98.6018 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 : 1.397 ------------------------------------------------------------------------------- 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: 0.3980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.5143 r_free = 0.5143 target = 0.308594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.283536 restraints weight = 43968.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.290665 restraints weight = 24195.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.295476 restraints weight = 15324.753| |-----------------------------------------------------------------------------| r_work (final): 0.5027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10358 Z= 0.129 Angle : 0.530 6.388 14062 Z= 0.294 Chirality : 0.037 0.142 1586 Planarity : 0.004 0.046 1718 Dihedral : 4.541 24.279 1376 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.56 % Allowed : 8.65 % Favored : 90.79 % 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: 0.14 (0.24), residues: 1250 helix: 0.76 (0.18), residues: 788 sheet: 0.30 (1.05), residues: 20 loop : -1.05 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 286 HIS 0.006 0.001 HIS A 739 PHE 0.026 0.002 PHE A 157 TYR 0.012 0.001 TYR B 147 ARG 0.005 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 590) hydrogen bonds : angle 5.02650 ( 1746) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.40330 ( 12) covalent geometry : bond 0.00270 (10352) covalent geometry : angle 0.53003 (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 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.340 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: B 457 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7304 (tttt) REVERT: B 693 MET cc_start: 0.6017 (mmm) cc_final: 0.5649 (mtp) outliers start: 6 outliers final: 6 residues processed: 148 average time/residue: 0.4701 time to fit residues: 98.7145 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.305767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.279795 restraints weight = 44302.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.286923 restraints weight = 24878.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.291737 restraints weight = 15889.853| |-----------------------------------------------------------------------------| r_work (final): 0.4997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4642 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10358 Z= 0.159 Angle : 0.556 7.860 14062 Z= 0.310 Chirality : 0.038 0.145 1586 Planarity : 0.005 0.046 1718 Dihedral : 4.552 22.662 1376 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.94 % Allowed : 9.87 % Favored : 89.19 % 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: 0.11 (0.24), residues: 1250 helix: 0.74 (0.18), residues: 784 sheet: 0.08 (1.04), residues: 20 loop : -1.04 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 286 HIS 0.005 0.001 HIS A 223 PHE 0.027 0.002 PHE A 157 TYR 0.017 0.001 TYR B 278 ARG 0.005 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 590) hydrogen bonds : angle 5.05906 ( 1746) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.45238 ( 12) covalent geometry : bond 0.00340 (10352) covalent geometry : angle 0.55621 (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 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.407 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: B 383 TYR cc_start: 0.3719 (m-80) cc_final: 0.2966 (m-10) REVERT: B 693 MET cc_start: 0.6013 (mmm) cc_final: 0.5644 (mtp) outliers start: 10 outliers final: 10 residues processed: 147 average time/residue: 0.4766 time to fit residues: 99.0639 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 525 MET 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: 7.9990 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.297111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.269075 restraints weight = 45249.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.275794 restraints weight = 26164.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.280515 restraints weight = 17418.690| |-----------------------------------------------------------------------------| r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10358 Z= 0.255 Angle : 0.704 9.111 14062 Z= 0.401 Chirality : 0.043 0.203 1586 Planarity : 0.006 0.067 1718 Dihedral : 5.326 26.025 1376 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.97 % Allowed : 12.88 % Favored : 85.15 % 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: -0.76 (0.23), residues: 1250 helix: 0.03 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 286 HIS 0.008 0.002 HIS A 223 PHE 0.042 0.003 PHE A 534 TYR 0.023 0.002 TYR B 278 ARG 0.006 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 590) hydrogen bonds : angle 5.70488 ( 1746) SS BOND : bond 0.00525 ( 6) SS BOND : angle 0.74056 ( 12) covalent geometry : bond 0.00550 (10352) covalent geometry : angle 0.70446 (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 164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.582 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: 0.6737 (mm-30) cc_final: 0.5884 (mm-30) REVERT: B 383 TYR cc_start: 0.3924 (m-80) cc_final: 0.3019 (m-10) REVERT: B 693 MET cc_start: 0.6048 (mmm) cc_final: 0.5659 (mtp) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.4978 time to fit residues: 106.8074 Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 594 MET 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: 6.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 0.0030 chunk 42 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.5134 r_free = 0.5134 target = 0.306128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.281008 restraints weight = 44828.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.287637 restraints weight = 25652.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.292310 restraints weight = 16891.328| |-----------------------------------------------------------------------------| r_work (final): 0.5011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4730 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10358 Z= 0.130 Angle : 0.548 6.161 14062 Z= 0.302 Chirality : 0.038 0.146 1586 Planarity : 0.004 0.043 1718 Dihedral : 4.692 23.094 1376 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.94 % Allowed : 14.19 % Favored : 84.87 % 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: -0.19 (0.24), residues: 1250 helix: 0.58 (0.18), residues: 788 sheet: 0.05 (1.11), residues: 20 loop : -1.36 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 497 HIS 0.005 0.001 HIS A 223 PHE 0.029 0.002 PHE A 157 TYR 0.017 0.001 TYR B 278 ARG 0.003 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 590) hydrogen bonds : angle 5.00070 ( 1746) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.42559 ( 12) covalent geometry : bond 0.00278 (10352) covalent geometry : angle 0.54839 (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 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.361 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: 0.6421 (mm-30) cc_final: 0.5644 (mm-30) REVERT: B 383 TYR cc_start: 0.3810 (m-80) cc_final: 0.2985 (m-10) REVERT: B 457 LYS cc_start: 0.8233 (ttmt) cc_final: 0.8026 (ttmt) REVERT: B 693 MET cc_start: 0.6125 (mmm) cc_final: 0.5689 (mtp) outliers start: 10 outliers final: 9 residues processed: 149 average time/residue: 0.4894 time to fit residues: 103.7357 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.294541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.265582 restraints weight = 43680.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.272738 restraints weight = 24649.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.277646 restraints weight = 16041.583| |-----------------------------------------------------------------------------| r_work (final): 0.4887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5030 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10358 Z= 0.293 Angle : 0.724 6.660 14062 Z= 0.415 Chirality : 0.043 0.225 1586 Planarity : 0.006 0.053 1718 Dihedral : 5.476 30.080 1376 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.44 % Allowed : 14.29 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -1.10 (0.23), residues: 1250 helix: -0.16 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 286 HIS 0.009 0.002 HIS A 223 PHE 0.042 0.003 PHE A 534 TYR 0.023 0.002 TYR B 278 ARG 0.005 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 590) hydrogen bonds : angle 5.84264 ( 1746) SS BOND : bond 0.00584 ( 6) SS BOND : angle 0.82513 ( 12) covalent geometry : bond 0.00625 (10352) covalent geometry : angle 0.72439 (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 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.413 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: A 535 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6016 (mm-30) REVERT: B 300 ARG cc_start: 0.5894 (ttt180) cc_final: 0.5286 (ttp-170) REVERT: B 693 MET cc_start: 0.6119 (mmm) cc_final: 0.5914 (mtp) outliers start: 26 outliers final: 22 residues processed: 142 average time/residue: 0.4858 time to fit residues: 97.2397 Evaluate side-chains 148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 129 TRP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 205 LEU 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 563 GLU Chi-restraints excluded: chain B residue 594 MET 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: 0.2980 chunk 108 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 569 HIS B 569 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.302919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.276944 restraints weight = 44674.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.283857 restraints weight = 24825.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.288770 restraints weight = 16056.513| |-----------------------------------------------------------------------------| r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4797 moved from start: 0.3651 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= 0.136 Angle : 0.561 6.096 14062 Z= 0.310 Chirality : 0.038 0.150 1586 Planarity : 0.005 0.051 1718 Dihedral : 4.829 22.985 1376 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.32 % Allowed : 15.60 % 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: -0.41 (0.24), residues: 1250 helix: 0.46 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.49 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 286 HIS 0.006 0.001 HIS A 569 PHE 0.037 0.002 PHE A 157 TYR 0.019 0.001 TYR B 278 ARG 0.002 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 590) hydrogen bonds : angle 5.13404 ( 1746) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.50991 ( 12) covalent geometry : bond 0.00293 (10352) covalent geometry : angle 0.56054 (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 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.515 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: 0.6517 (mm-30) cc_final: 0.5737 (mm-30) REVERT: B 693 MET cc_start: 0.6101 (mmm) cc_final: 0.5895 (mtp) outliers start: 14 outliers final: 11 residues processed: 149 average time/residue: 0.5076 time to fit residues: 107.8965 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 701 HIS 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 594 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 67 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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 = 0.5075 r_free = 0.5075 target = 0.298730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.270858 restraints weight = 43864.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.278386 restraints weight = 24112.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.283244 restraints weight = 15315.246| |-----------------------------------------------------------------------------| r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4881 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10358 Z= 0.182 Angle : 0.597 7.082 14062 Z= 0.338 Chirality : 0.039 0.202 1586 Planarity : 0.005 0.056 1718 Dihedral : 4.879 21.747 1376 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.60 % Allowed : 15.51 % Favored : 82.89 % 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: -0.54 (0.24), residues: 1250 helix: 0.34 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.004 0.001 HIS A 569 PHE 0.035 0.002 PHE A 157 TYR 0.020 0.002 TYR B 278 ARG 0.003 0.000 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 590) hydrogen bonds : angle 5.26554 ( 1746) SS BOND : bond 0.00359 ( 6) SS BOND : angle 0.62354 ( 12) covalent geometry : bond 0.00396 (10352) covalent geometry : angle 0.59715 (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 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.505 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: A 535 GLU cc_start: 0.6817 (mm-30) cc_final: 0.5937 (mm-30) REVERT: A 740 MET cc_start: 0.6612 (ptp) cc_final: 0.6330 (ptp) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.4898 time to fit residues: 103.0041 Evaluate side-chains 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 407 LEU Chi-restraints excluded: chain A residue 525 MET 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: 5.9990 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.5103 r_free = 0.5103 target = 0.302688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.276131 restraints weight = 44950.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.283336 restraints weight = 25154.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.288126 restraints weight = 16241.688| |-----------------------------------------------------------------------------| r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4804 moved from start: 0.3992 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= 0.141 Angle : 0.558 6.508 14062 Z= 0.310 Chirality : 0.037 0.145 1586 Planarity : 0.005 0.054 1718 Dihedral : 4.690 21.683 1376 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.22 % Allowed : 15.60 % Favored : 83.18 % 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: -0.28 (0.24), residues: 1250 helix: 0.58 (0.18), residues: 788 sheet: 0.28 (1.18), residues: 20 loop : -1.55 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 286 HIS 0.005 0.001 HIS A 569 PHE 0.036 0.002 PHE A 157 TYR 0.018 0.001 TYR B 278 ARG 0.003 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 590) hydrogen bonds : angle 5.03215 ( 1746) SS BOND : bond 0.00520 ( 6) SS BOND : angle 0.48457 ( 12) covalent geometry : bond 0.00306 (10352) covalent geometry : angle 0.55842 (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 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.564 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: 0.6608 (mm-30) cc_final: 0.5744 (mm-30) REVERT: A 740 MET cc_start: 0.6635 (ptp) cc_final: 0.6367 (ptp) outliers start: 13 outliers final: 12 residues processed: 150 average time/residue: 0.4972 time to fit residues: 105.2672 Evaluate side-chains 149 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 CYS 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 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 50 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 overall best weight: 1.6942 ------------------------------------------------------------------------------- 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 = 0.5076 r_free = 0.5076 target = 0.298901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.271023 restraints weight = 44223.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.278546 restraints weight = 24144.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.283567 restraints weight = 15239.742| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4868 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10358 Z= 0.172 Angle : 0.582 6.422 14062 Z= 0.328 Chirality : 0.038 0.150 1586 Planarity : 0.005 0.052 1718 Dihedral : 4.748 21.174 1376 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.13 % Allowed : 16.17 % Favored : 82.71 % 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: 0.51 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.004 0.001 HIS B 223 PHE 0.036 0.002 PHE A 157 TYR 0.019 0.001 TYR B 278 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 590) hydrogen bonds : angle 5.16534 ( 1746) SS BOND : bond 0.00403 ( 6) SS BOND : angle 0.54975 ( 12) covalent geometry : bond 0.00375 (10352) covalent geometry : angle 0.58239 (14050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5495.04 seconds wall clock time: 95 minutes 54.63 seconds (5754.63 seconds total)