Starting phenix.real_space_refine on Sat Dec 28 13:15:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxf_21436/12_2024/6vxf_21436.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5700 2.51 5 N 1450 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8786 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4393 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 8.11, per 1000 atoms: 0.92 Number of scatterers: 8786 At special positions: 0 Unit cell: (99.63, 73.8, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1578 8.00 N 1450 7.00 C 5700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 60.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.656A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.668A pdb=" N GLY B 101 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 102 " --> pdb=" O PRO B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.784A pdb=" N PHE B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.877A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.815A pdb=" N PHE B 250 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 251' Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.057A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.735A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.780A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 4.120A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 395 through 415 removed outlier: 3.941A pdb=" N GLY B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 435 removed outlier: 3.861A pdb=" N GLY B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 445 removed outlier: 4.714A pdb=" N PHE B 439 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 440 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 441 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 442 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.583A pdb=" N HIS B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 504 through 528 removed outlier: 3.670A pdb=" N ALA B 528 " --> pdb=" O ALA B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 546 removed outlier: 3.912A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.562A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.653A pdb=" N LEU B 568 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 4.237A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.800A pdb=" N VAL B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.717A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.657A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.668A pdb=" N GLY A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.784A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.877A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.814A pdb=" N PHE A 250 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.057A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.736A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.780A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 4.120A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 395 through 415 removed outlier: 3.942A pdb=" N GLY A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.860A pdb=" N GLY A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 4.714A pdb=" N PHE A 439 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 442 " --> pdb=" O PHE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.584A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 504 through 528 removed outlier: 3.671A pdb=" N ALA A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 removed outlier: 3.912A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.562A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.654A pdb=" N LEU A 568 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 4.237A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.801A pdb=" N VAL A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.718A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'B' and resid 121 through 123 removed outlier: 5.788A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 removed outlier: 5.788A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2746 1.34 - 1.46: 2171 1.46 - 1.59: 3957 1.59 - 1.71: 0 1.71 - 1.83: 94 Bond restraints: 8968 Sorted by residual: bond pdb=" CA LEU B 497 " pdb=" CB LEU B 497 " ideal model delta sigma weight residual 1.542 1.519 0.024 8.90e-03 1.26e+04 7.12e+00 bond pdb=" CA LEU A 497 " pdb=" CB LEU A 497 " ideal model delta sigma weight residual 1.542 1.519 0.023 8.90e-03 1.26e+04 6.74e+00 bond pdb=" CG LEU B 209 " pdb=" CD1 LEU B 209 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CG LEU A 209 " pdb=" CD1 LEU A 209 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CG LEU A 474 " pdb=" CD2 LEU A 474 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 ... (remaining 8963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11620 2.25 - 4.49: 415 4.49 - 6.74: 75 6.74 - 8.98: 20 8.98 - 11.23: 4 Bond angle restraints: 12134 Sorted by residual: angle pdb=" N LEU A 497 " pdb=" CA LEU A 497 " pdb=" C LEU A 497 " ideal model delta sigma weight residual 108.49 114.24 -5.75 1.15e+00 7.56e-01 2.50e+01 angle pdb=" N LEU B 497 " pdb=" CA LEU B 497 " pdb=" C LEU B 497 " ideal model delta sigma weight residual 108.49 114.23 -5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" C ALA A 95 " pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ALA B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C LEU A 497 " pdb=" CA LEU A 497 " pdb=" CB LEU A 497 " ideal model delta sigma weight residual 114.87 109.20 5.67 1.51e+00 4.39e-01 1.41e+01 ... (remaining 12129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4658 17.86 - 35.73: 531 35.73 - 53.59: 94 53.59 - 71.45: 20 71.45 - 89.32: 6 Dihedral angle restraints: 5309 sinusoidal: 2057 harmonic: 3252 Sorted by residual: dihedral pdb=" CA LEU B 555 " pdb=" C LEU B 555 " pdb=" N VAL B 556 " pdb=" CA VAL B 556 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LEU A 555 " pdb=" C LEU A 555 " pdb=" N VAL A 556 " pdb=" CA VAL A 556 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU A 138 " pdb=" C GLU A 138 " pdb=" N ASN A 139 " pdb=" CA ASN A 139 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 5306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 878 0.048 - 0.096: 404 0.096 - 0.143: 92 0.143 - 0.191: 22 0.191 - 0.239: 12 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR B 609 " pdb=" CA THR B 609 " pdb=" OG1 THR B 609 " pdb=" CG2 THR B 609 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR A 609 " pdb=" CA THR A 609 " pdb=" OG1 THR A 609 " pdb=" CG2 THR A 609 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1405 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 545 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C PHE B 545 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE B 545 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL B 546 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 545 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C PHE A 545 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE A 545 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 546 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 622 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 623 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " 0.030 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 72 2.60 - 3.18: 7230 3.18 - 3.75: 13732 3.75 - 4.33: 18935 4.33 - 4.90: 31710 Nonbonded interactions: 71679 Sorted by model distance: nonbonded pdb=" SG CYS B 603 " pdb=" SG CYS A 603 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " model vdw 2.039 3.760 nonbonded pdb=" O SER A 552 " pdb=" OG SER A 552 " model vdw 2.255 3.040 nonbonded pdb=" O SER B 552 " pdb=" OG SER B 552 " model vdw 2.255 3.040 nonbonded pdb=" O MET A 548 " pdb=" OG SER A 552 " model vdw 2.333 3.040 ... (remaining 71674 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 8968 Z= 0.604 Angle : 1.040 11.230 12134 Z= 0.550 Chirality : 0.059 0.239 1408 Planarity : 0.006 0.053 1514 Dihedral : 15.362 89.316 3218 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 1.25 % Allowed : 10.50 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.65 (0.18), residues: 1114 helix: -2.83 (0.14), residues: 606 sheet: -2.77 (0.70), residues: 50 loop : -3.35 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 379 HIS 0.010 0.002 HIS B 155 PHE 0.018 0.003 PHE A 182 TYR 0.026 0.003 TYR A 494 ARG 0.003 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.457 Fit side-chains REVERT: B 163 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6795 (ttm170) REVERT: B 246 ARG cc_start: 0.8063 (ptp-170) cc_final: 0.7705 (ptp-110) REVERT: B 515 MET cc_start: 0.8633 (mmm) cc_final: 0.8156 (mmp) REVERT: B 628 LYS cc_start: 0.7596 (tttt) cc_final: 0.7302 (ttpp) REVERT: A 126 GLN cc_start: 0.8247 (tt0) cc_final: 0.7945 (tt0) REVERT: A 194 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (t) REVERT: A 382 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8742 (ttmm) REVERT: A 515 MET cc_start: 0.8640 (mmm) cc_final: 0.7832 (mmp) REVERT: A 541 MET cc_start: 0.9071 (tpp) cc_final: 0.8813 (tpt) REVERT: A 623 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8507 (Cg_endo) REVERT: A 628 LYS cc_start: 0.7452 (tttt) cc_final: 0.7213 (ttmt) outliers start: 12 outliers final: 2 residues processed: 161 average time/residue: 0.2242 time to fit residues: 49.5528 Evaluate side-chains 121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 609 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN B 271 GLN B 629 ASN A 158 ASN A 166 GLN A 629 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.170 Angle : 0.608 7.631 12134 Z= 0.312 Chirality : 0.041 0.137 1408 Planarity : 0.004 0.032 1514 Dihedral : 5.742 42.825 1207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.94 % Allowed : 16.53 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.23), residues: 1114 helix: -0.76 (0.20), residues: 596 sheet: -2.01 (0.58), residues: 70 loop : -2.77 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.008 0.001 HIS B 155 PHE 0.016 0.001 PHE A 470 TYR 0.015 0.001 TYR A 342 ARG 0.005 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: B 163 ARG cc_start: 0.7073 (ttp-170) cc_final: 0.6647 (ttm170) REVERT: B 342 TYR cc_start: 0.6741 (t80) cc_final: 0.6534 (t80) REVERT: B 509 MET cc_start: 0.8297 (ttm) cc_final: 0.8095 (ttp) REVERT: B 514 MET cc_start: 0.8250 (mtt) cc_final: 0.8035 (mtm) REVERT: B 515 MET cc_start: 0.8552 (mmm) cc_final: 0.8199 (mmp) REVERT: B 628 LYS cc_start: 0.7511 (tttt) cc_final: 0.7218 (ttpp) REVERT: A 168 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 272 GLU cc_start: 0.7180 (pm20) cc_final: 0.6787 (pm20) REVERT: A 382 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8694 (ttmm) REVERT: A 458 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 471 LEU cc_start: 0.8672 (mp) cc_final: 0.8365 (mt) REVERT: A 515 MET cc_start: 0.8485 (mmm) cc_final: 0.7684 (mmp) REVERT: A 570 TYR cc_start: 0.8685 (m-80) cc_final: 0.8141 (m-80) REVERT: A 628 LYS cc_start: 0.7355 (tttt) cc_final: 0.7037 (ttmt) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.2131 time to fit residues: 43.9239 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 609 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8968 Z= 0.284 Angle : 0.635 7.391 12134 Z= 0.323 Chirality : 0.043 0.174 1408 Planarity : 0.003 0.030 1514 Dihedral : 5.195 22.449 1206 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 2.29 % Allowed : 17.57 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.25), residues: 1114 helix: -0.03 (0.21), residues: 596 sheet: -2.24 (0.53), residues: 70 loop : -2.55 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 PHE 0.011 0.002 PHE B 470 TYR 0.014 0.002 TYR A 459 ARG 0.012 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.994 Fit side-chains REVERT: B 45 ARG cc_start: 0.6008 (ttt-90) cc_final: 0.5767 (ttt90) REVERT: B 258 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7643 (tp) REVERT: B 487 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 509 MET cc_start: 0.8599 (ttm) cc_final: 0.8342 (ttm) REVERT: B 515 MET cc_start: 0.8642 (mmm) cc_final: 0.8171 (mmp) REVERT: B 541 MET cc_start: 0.8430 (tpt) cc_final: 0.8003 (tpt) REVERT: B 628 LYS cc_start: 0.7528 (tttt) cc_final: 0.7227 (ttpp) REVERT: A 193 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7910 (ttm110) REVERT: A 258 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 272 GLU cc_start: 0.7156 (pm20) cc_final: 0.6895 (pm20) REVERT: A 382 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8741 (ttmm) REVERT: A 487 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8534 (mt) REVERT: A 515 MET cc_start: 0.8498 (mmm) cc_final: 0.7622 (mmp) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.2317 time to fit residues: 47.4412 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN A 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8968 Z= 0.233 Angle : 0.596 6.855 12134 Z= 0.301 Chirality : 0.042 0.185 1408 Planarity : 0.003 0.037 1514 Dihedral : 4.977 22.330 1204 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.01 % Allowed : 19.54 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.25), residues: 1114 helix: 0.41 (0.22), residues: 598 sheet: -2.30 (0.51), residues: 70 loop : -2.49 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 267 PHE 0.017 0.001 PHE B 506 TYR 0.013 0.001 TYR A 459 ARG 0.006 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.933 Fit side-chains REVERT: B 258 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 487 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 509 MET cc_start: 0.8566 (ttm) cc_final: 0.8193 (ttt) REVERT: B 515 MET cc_start: 0.8639 (mmm) cc_final: 0.8118 (mmp) REVERT: B 541 MET cc_start: 0.8402 (tpt) cc_final: 0.8063 (tpt) REVERT: B 573 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8914 (mp) REVERT: A 193 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7856 (ttm110) REVERT: A 258 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7937 (tt) REVERT: A 272 GLU cc_start: 0.7131 (pm20) cc_final: 0.6830 (pm20) REVERT: A 382 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8735 (ttmm) REVERT: A 475 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8359 (tt) REVERT: A 515 MET cc_start: 0.8529 (mmm) cc_final: 0.7622 (mmp) REVERT: A 554 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7698 (pt) outliers start: 29 outliers final: 17 residues processed: 162 average time/residue: 0.2319 time to fit residues: 50.8428 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8968 Z= 0.240 Angle : 0.591 8.084 12134 Z= 0.300 Chirality : 0.041 0.136 1408 Planarity : 0.003 0.028 1514 Dihedral : 4.858 21.804 1204 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.64 % Allowed : 20.06 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1114 helix: 0.66 (0.22), residues: 598 sheet: -2.33 (0.50), residues: 70 loop : -2.46 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 267 PHE 0.017 0.001 PHE B 506 TYR 0.026 0.001 TYR A 247 ARG 0.006 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.102 Fit side-chains REVERT: B 107 LEU cc_start: 0.8299 (tt) cc_final: 0.8016 (mp) REVERT: B 258 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 475 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 487 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8270 (mt) REVERT: B 515 MET cc_start: 0.8628 (mmm) cc_final: 0.8120 (mmp) REVERT: B 541 MET cc_start: 0.8387 (tpt) cc_final: 0.8052 (tpt) REVERT: B 573 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8935 (mp) REVERT: A 191 ARG cc_start: 0.6765 (ttt180) cc_final: 0.6198 (ttt90) REVERT: A 193 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7911 (ttm110) REVERT: A 258 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 265 MET cc_start: 0.7880 (mmp) cc_final: 0.7631 (mmp) REVERT: A 272 GLU cc_start: 0.7249 (pm20) cc_final: 0.6926 (pm20) REVERT: A 382 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8730 (ttmm) REVERT: A 475 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 515 MET cc_start: 0.8549 (mmm) cc_final: 0.7543 (mmp) outliers start: 35 outliers final: 23 residues processed: 156 average time/residue: 0.2111 time to fit residues: 45.7381 Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8968 Z= 0.193 Angle : 0.562 8.521 12134 Z= 0.285 Chirality : 0.040 0.134 1408 Planarity : 0.003 0.027 1514 Dihedral : 4.705 21.731 1204 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.33 % Allowed : 20.79 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.26), residues: 1114 helix: 0.93 (0.22), residues: 598 sheet: -2.23 (0.50), residues: 70 loop : -2.35 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.001 PHE B 506 TYR 0.022 0.001 TYR B 342 ARG 0.007 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.967 Fit side-chains REVERT: B 107 LEU cc_start: 0.8282 (tt) cc_final: 0.7999 (mp) REVERT: B 181 GLN cc_start: 0.5651 (mp10) cc_final: 0.5290 (mp10) REVERT: B 193 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7159 (mtt-85) REVERT: B 258 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7809 (tt) REVERT: B 454 LEU cc_start: 0.9304 (tp) cc_final: 0.8992 (tp) REVERT: B 515 MET cc_start: 0.8619 (mmm) cc_final: 0.8115 (mmp) REVERT: B 541 MET cc_start: 0.8362 (tpt) cc_final: 0.8055 (tpt) REVERT: A 191 ARG cc_start: 0.6723 (ttt180) cc_final: 0.6488 (ttt-90) REVERT: A 193 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7951 (ttm110) REVERT: A 258 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 272 GLU cc_start: 0.7137 (pm20) cc_final: 0.6778 (pm20) REVERT: A 382 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8767 (ttmm) REVERT: A 515 MET cc_start: 0.8577 (mmm) cc_final: 0.7604 (mmp) outliers start: 32 outliers final: 21 residues processed: 164 average time/residue: 0.2241 time to fit residues: 50.7566 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8968 Z= 0.307 Angle : 0.630 9.600 12134 Z= 0.317 Chirality : 0.043 0.156 1408 Planarity : 0.003 0.042 1514 Dihedral : 4.808 20.988 1204 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 3.22 % Allowed : 21.41 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.26), residues: 1114 helix: 0.76 (0.22), residues: 598 sheet: -2.32 (0.49), residues: 70 loop : -2.36 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 PHE 0.018 0.002 PHE B 506 TYR 0.018 0.002 TYR B 342 ARG 0.006 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 107 LEU cc_start: 0.8291 (tt) cc_final: 0.8050 (mp) REVERT: B 193 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7161 (mtt-85) REVERT: B 258 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7935 (tp) REVERT: B 515 MET cc_start: 0.8648 (mmm) cc_final: 0.8173 (mmp) REVERT: B 541 MET cc_start: 0.8347 (tpt) cc_final: 0.8086 (tpt) REVERT: A 191 ARG cc_start: 0.6716 (ttt180) cc_final: 0.6494 (ttt-90) REVERT: A 258 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8003 (tt) REVERT: A 272 GLU cc_start: 0.7173 (pm20) cc_final: 0.6935 (pm20) REVERT: A 515 MET cc_start: 0.8583 (mmm) cc_final: 0.7575 (mmp) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.2306 time to fit residues: 48.5088 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8968 Z= 0.214 Angle : 0.590 9.122 12134 Z= 0.297 Chirality : 0.041 0.213 1408 Planarity : 0.003 0.027 1514 Dihedral : 4.704 21.320 1204 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.12 % Allowed : 21.73 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.26), residues: 1114 helix: 0.95 (0.22), residues: 598 sheet: -2.23 (0.49), residues: 70 loop : -2.27 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.005 0.001 HIS A 155 PHE 0.019 0.001 PHE A 506 TYR 0.023 0.001 TYR B 342 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.028 Fit side-chains REVERT: B 107 LEU cc_start: 0.8262 (tt) cc_final: 0.8031 (mp) REVERT: B 181 GLN cc_start: 0.5784 (mp10) cc_final: 0.5359 (mp10) REVERT: B 193 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7131 (mtt-85) REVERT: B 246 ARG cc_start: 0.7739 (ptp-110) cc_final: 0.7083 (mtp85) REVERT: B 258 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 424 GLN cc_start: 0.7460 (tp40) cc_final: 0.7255 (mm-40) REVERT: B 515 MET cc_start: 0.8622 (mmm) cc_final: 0.7676 (mmp) REVERT: A 193 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7451 (mtt-85) REVERT: A 258 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 272 GLU cc_start: 0.7186 (pm20) cc_final: 0.6964 (pm20) REVERT: A 515 MET cc_start: 0.8573 (mmm) cc_final: 0.7579 (mmp) outliers start: 30 outliers final: 24 residues processed: 153 average time/residue: 0.2199 time to fit residues: 46.5511 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8968 Z= 0.204 Angle : 0.576 8.573 12134 Z= 0.291 Chirality : 0.041 0.153 1408 Planarity : 0.003 0.027 1514 Dihedral : 4.645 21.183 1204 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.01 % Allowed : 22.14 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.26), residues: 1114 helix: 1.03 (0.22), residues: 598 sheet: -2.15 (0.50), residues: 70 loop : -2.20 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.018 0.001 PHE A 506 TYR 0.022 0.001 TYR B 342 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.050 Fit side-chains REVERT: B 181 GLN cc_start: 0.5889 (mp10) cc_final: 0.5410 (mp10) REVERT: B 193 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7132 (mtt-85) REVERT: B 246 ARG cc_start: 0.7807 (ptp-110) cc_final: 0.7089 (mtp85) REVERT: B 258 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (tt) REVERT: B 515 MET cc_start: 0.8650 (mmm) cc_final: 0.7668 (mmp) REVERT: A 258 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 272 GLU cc_start: 0.7188 (pm20) cc_final: 0.6966 (pm20) REVERT: A 515 MET cc_start: 0.8577 (mmm) cc_final: 0.7596 (mmp) outliers start: 29 outliers final: 24 residues processed: 155 average time/residue: 0.2114 time to fit residues: 45.6483 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8968 Z= 0.201 Angle : 0.579 8.420 12134 Z= 0.290 Chirality : 0.041 0.170 1408 Planarity : 0.003 0.028 1514 Dihedral : 4.579 21.196 1204 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.91 % Allowed : 21.93 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.26), residues: 1114 helix: 1.11 (0.22), residues: 598 sheet: -2.06 (0.50), residues: 70 loop : -2.13 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.006 0.001 HIS A 155 PHE 0.019 0.001 PHE A 506 TYR 0.021 0.001 TYR B 342 ARG 0.008 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.035 Fit side-chains REVERT: B 193 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7171 (mtt-85) REVERT: B 246 ARG cc_start: 0.7812 (ptp-110) cc_final: 0.7075 (mtp85) REVERT: B 258 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 471 LEU cc_start: 0.8585 (mp) cc_final: 0.8345 (mt) REVERT: B 515 MET cc_start: 0.8645 (mmm) cc_final: 0.7680 (mmp) REVERT: B 541 MET cc_start: 0.8138 (tpt) cc_final: 0.7644 (tpt) REVERT: A 191 ARG cc_start: 0.6720 (ttt180) cc_final: 0.6155 (ttt90) REVERT: A 193 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7419 (mtt-85) REVERT: A 258 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 265 MET cc_start: 0.7920 (mmp) cc_final: 0.7642 (mmp) REVERT: A 272 GLU cc_start: 0.7227 (pm20) cc_final: 0.7014 (pm20) REVERT: A 515 MET cc_start: 0.8576 (mmm) cc_final: 0.7588 (mmp) outliers start: 28 outliers final: 26 residues processed: 153 average time/residue: 0.2129 time to fit residues: 45.1515 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.164590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126776 restraints weight = 11130.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.129116 restraints weight = 7854.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130442 restraints weight = 6409.296| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8968 Z= 0.186 Angle : 0.563 8.120 12134 Z= 0.283 Chirality : 0.040 0.165 1408 Planarity : 0.003 0.030 1514 Dihedral : 4.505 21.295 1204 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.22 % Allowed : 21.93 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.26), residues: 1114 helix: 1.21 (0.22), residues: 598 sheet: -2.00 (0.51), residues: 70 loop : -2.06 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.016 0.001 PHE A 506 TYR 0.021 0.001 TYR B 342 ARG 0.008 0.000 ARG A 193 =============================================================================== Job complete usr+sys time: 1783.27 seconds wall clock time: 33 minutes 35.39 seconds (2015.39 seconds total)