Starting phenix.real_space_refine on Sat Sep 28 19:14:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_36245.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_36245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_36245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_36245.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgs_36245/09_2024/8jgs_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-5461/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: 10.05, per 1000 atoms: 0.50 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: 5.56 Conformation dependent library (CDL) restraints added in 1.5 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: 1.75 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: 6.98 Time building geometry restraints manager: 6.59 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: 0.00 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: 1.140 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: 0.320 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.710 Find NCS groups from input model: 0.400 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: 0.000 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: 49.360 ------------------------------------------------------------------------------- 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 10352 Z= 0.192 Angle : 0.568 5.013 14050 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.590 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: 0.5186 time to fit residues: 109.1905 Evaluate side-chains 124 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4618 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 10352 Z= 0.252 Angle : 0.611 6.017 14050 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.437 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: 0.8064 (ttmt) cc_final: 0.7409 (tttt) REVERT: B 693 MET cc_start: 0.6456 (mmm) cc_final: 0.5869 (mtp) outliers start: 8 outliers final: 6 residues processed: 148 average time/residue: 0.4787 time to fit residues: 100.9597 Evaluate side-chains 136 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 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 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 63 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.0010 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10352 Z= 0.178 Angle : 0.535 6.352 14050 Z= 0.297 Chirality : 0.037 0.144 1586 Planarity : 0.004 0.046 1718 Dihedral : 4.572 24.227 1376 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.66 % Allowed : 8.83 % Favored : 90.51 % 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: 0.73 (0.18), residues: 788 sheet: 0.27 (1.05), residues: 20 loop : -1.07 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 286 HIS 0.005 0.001 HIS A 223 PHE 0.032 0.002 PHE A 157 TYR 0.013 0.001 TYR B 278 ARG 0.005 0.000 ARG A 247 *********************** 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 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.448 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 693 MET cc_start: 0.6047 (mmm) cc_final: 0.5697 (mtp) outliers start: 7 outliers final: 6 residues processed: 149 average time/residue: 0.4880 time to fit residues: 103.6769 Evaluate side-chains 140 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 113 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10352 Z= 0.191 Angle : 0.539 7.388 14050 Z= 0.298 Chirality : 0.037 0.144 1586 Planarity : 0.004 0.046 1718 Dihedral : 4.482 22.406 1376 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.85 % Allowed : 10.06 % Favored : 89.10 % 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: 0.21 (0.24), residues: 1250 helix: 0.79 (0.18), residues: 788 sheet: 0.07 (1.04), residues: 20 loop : -0.95 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 286 HIS 0.005 0.001 HIS A 223 PHE 0.030 0.002 PHE A 157 TYR 0.015 0.001 TYR B 278 ARG 0.004 0.000 ARG A 475 *********************** 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 151 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.593 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 243 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6878 (mm-30) REVERT: B 383 TYR cc_start: 0.3722 (m-80) cc_final: 0.2970 (m-10) REVERT: B 693 MET cc_start: 0.6038 (mmm) cc_final: 0.5687 (mtp) outliers start: 9 outliers final: 9 residues processed: 147 average time/residue: 0.4924 time to fit residues: 103.5484 Evaluate side-chains 144 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4831 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 10352 Z= 0.326 Angle : 0.648 7.020 14050 Z= 0.369 Chirality : 0.041 0.167 1586 Planarity : 0.005 0.047 1718 Dihedral : 5.010 23.793 1376 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.16 % Allowed : 12.12 % Favored : 85.71 % 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: -0.43 (0.24), residues: 1250 helix: 0.29 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -1.13 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 286 HIS 0.007 0.001 HIS A 223 PHE 0.037 0.002 PHE A 534 TYR 0.021 0.002 TYR B 278 ARG 0.005 0.000 ARG A 475 *********************** 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 161 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.475 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 243 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7074 (mm-30) REVERT: A 247 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6801 (mmt-90) REVERT: A 619 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5289 (ptt) REVERT: B 383 TYR cc_start: 0.3912 (m-80) cc_final: 0.3051 (m-10) REVERT: B 693 MET cc_start: 0.6119 (mmm) cc_final: 0.5750 (mtp) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 0.5075 time to fit residues: 106.4100 Evaluate side-chains 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 388 THR Chi-restraints excluded: chain A residue 522 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 0.0570 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4819 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10352 Z= 0.267 Angle : 0.598 5.961 14050 Z= 0.338 Chirality : 0.039 0.156 1586 Planarity : 0.005 0.044 1718 Dihedral : 4.945 23.924 1376 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.22 % Allowed : 14.38 % Favored : 84.40 % 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: -0.52 (0.24), residues: 1250 helix: 0.27 (0.18), residues: 788 sheet: None (None), residues: 0 loop : -1.33 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 286 HIS 0.006 0.001 HIS A 223 PHE 0.029 0.002 PHE A 534 TYR 0.020 0.002 TYR B 278 ARG 0.004 0.000 ARG B 475 *********************** 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 156 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.451 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 243 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 383 TYR cc_start: 0.3941 (m-80) cc_final: 0.3052 (m-10) REVERT: B 693 MET cc_start: 0.6122 (mmm) cc_final: 0.5910 (mtp) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.5048 time to fit residues: 107.1475 Evaluate side-chains 142 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4684 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10352 Z= 0.167 Angle : 0.530 6.092 14050 Z= 0.291 Chirality : 0.037 0.146 1586 Planarity : 0.004 0.043 1718 Dihedral : 4.557 21.905 1376 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.22 % Allowed : 14.57 % Favored : 84.21 % 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: -0.01 (0.24), residues: 1250 helix: 0.71 (0.18), residues: 790 sheet: 0.14 (1.14), residues: 20 loop : -1.28 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 286 HIS 0.005 0.001 HIS B 569 PHE 0.032 0.002 PHE A 157 TYR 0.015 0.001 TYR B 278 ARG 0.002 0.000 ARG B 571 *********************** 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 158 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.378 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: 0.6436 (mm-30) cc_final: 0.5628 (mm-30) REVERT: B 383 TYR cc_start: 0.3778 (m-80) cc_final: 0.2985 (m-10) REVERT: B 457 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8043 (ttmt) outliers start: 13 outliers final: 7 residues processed: 152 average time/residue: 0.4895 time to fit residues: 104.4795 Evaluate side-chains 141 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10352 Z= 0.244 Angle : 0.574 6.154 14050 Z= 0.322 Chirality : 0.038 0.150 1586 Planarity : 0.005 0.049 1718 Dihedral : 4.711 22.541 1376 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.32 % Allowed : 14.47 % Favored : 84.21 % 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: -0.25 (0.24), residues: 1250 helix: 0.54 (0.18), residues: 790 sheet: 0.27 (1.18), residues: 20 loop : -1.42 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.006 0.001 HIS B 569 PHE 0.037 0.002 PHE A 157 TYR 0.019 0.001 TYR B 278 ARG 0.004 0.000 ARG A 475 *********************** 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 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.595 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: 0.6674 (mm-30) cc_final: 0.5855 (mm-30) REVERT: B 383 TYR cc_start: 0.3962 (m-80) cc_final: 0.3097 (m-10) REVERT: B 457 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8269 (ttmt) REVERT: B 740 MET cc_start: 0.6344 (ptp) cc_final: 0.6104 (ptp) outliers start: 14 outliers final: 12 residues processed: 153 average time/residue: 0.5104 time to fit residues: 109.2368 Evaluate side-chains 148 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 129 TRP 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 27 ILE 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 274 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4862 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10352 Z= 0.259 Angle : 0.597 6.014 14050 Z= 0.337 Chirality : 0.039 0.151 1586 Planarity : 0.005 0.052 1718 Dihedral : 4.855 21.810 1376 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.69 % Allowed : 14.29 % 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: -0.44 (0.24), residues: 1250 helix: 0.38 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 286 HIS 0.004 0.001 HIS A 223 PHE 0.033 0.002 PHE A 534 TYR 0.020 0.002 TYR B 278 ARG 0.003 0.000 ARG A 475 *********************** 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 157 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.431 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: 0.6742 (mm-30) cc_final: 0.5856 (mm-30) REVERT: A 740 MET cc_start: 0.6644 (ptp) cc_final: 0.6418 (ptp) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 0.5029 time to fit residues: 104.5614 Evaluate side-chains 149 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 129 TRP 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 249 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4807 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10352 Z= 0.202 Angle : 0.548 6.013 14050 Z= 0.305 Chirality : 0.037 0.148 1586 Planarity : 0.005 0.052 1718 Dihedral : 4.669 21.953 1376 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -0.23 (0.24), residues: 1250 helix: 0.57 (0.18), residues: 792 sheet: 0.20 (1.14), residues: 20 loop : -1.45 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.004 0.001 HIS A 223 PHE 0.037 0.002 PHE A 157 TYR 0.018 0.001 TYR B 278 ARG 0.003 0.000 ARG A 247 ********************** 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 153 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.452 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6567 (mm-30) cc_final: 0.5755 (mm-30) outliers start: 14 outliers final: 14 residues processed: 147 average time/residue: 0.5035 time to fit residues: 103.3731 Evaluate side-chains 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL 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 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 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 30 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.5097 r_free = 0.5097 target = 0.301385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.274313 restraints weight = 44355.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.281695 restraints weight = 24349.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.286699 restraints weight = 15340.559| |-----------------------------------------------------------------------------| r_work (final): 0.4958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4802 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10352 Z= 0.197 Angle : 0.548 6.721 14050 Z= 0.306 Chirality : 0.037 0.145 1586 Planarity : 0.005 0.051 1718 Dihedral : 4.592 20.989 1376 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.50 % Allowed : 14.85 % Favored : 83.65 % 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: -0.17 (0.24), residues: 1250 helix: 0.63 (0.18), residues: 792 sheet: 0.15 (1.14), residues: 20 loop : -1.44 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 286 HIS 0.004 0.001 HIS A 223 PHE 0.036 0.002 PHE A 157 TYR 0.017 0.001 TYR B 278 ARG 0.004 0.000 ARG A 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.03 seconds wall clock time: 70 minutes 24.34 seconds (4224.34 seconds total)