Starting phenix.real_space_refine on Sat Nov 16 11:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/11_2024/8k3c_36849.cif" } resolution = 2.88 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= 0.031 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 61 5.16 5 C 6844 2.51 5 N 1824 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10813 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1778 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 224} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3710 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 437} Chain: "B" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3718 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 438} Time building chain proxies: 10.07, per 1000 atoms: 0.93 Number of scatterers: 10813 At special positions: 0 Unit cell: (95.12, 109.88, 176.3, 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 61 16.00 O 2084 8.00 N 1824 7.00 C 6844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 197 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.02 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.01 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.02 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.02 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 27 sheets defined 7.5% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 125 through 131 removed outlier: 4.222A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.352A pdb=" N SER C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N CYS B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 121 removed outlier: 3.696A pdb=" N LEU D 182 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D 142 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR D 176 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.888A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR C 125 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.765A pdb=" N CYS C 214 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 227 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 216 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.744A pdb=" N LYS A 199 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A 596 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 216 through 224 removed outlier: 6.282A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.286A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB7, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.800A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.590A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 557 through 567 removed outlier: 3.922A pdb=" N ASN A 557 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU A 579 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR A 561 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 577 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR A 563 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 575 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 565 " --> pdb=" O TRP A 573 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP A 573 " --> pdb=" O CYS A 565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 178 through 179 removed outlier: 5.965A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 587 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.557A pdb=" N PHE B 229 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.398A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.808A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC8, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.512A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 465 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 511 through 513 removed outlier: 4.971A pdb=" N GLN B 550 " --> pdb=" O PRO B 535 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B 537 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 999 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: 3.79 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3412 1.34 - 1.46: 2844 1.46 - 1.59: 4744 1.59 - 1.72: 0 1.72 - 1.84: 78 Bond restraints: 11078 Sorted by residual: bond pdb=" C SER A 390 " pdb=" N LYS A 391 " ideal model delta sigma weight residual 1.329 1.237 0.091 1.60e-02 3.91e+03 3.25e+01 bond pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N ILE D 140 " pdb=" CA ILE D 140 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N VAL D 119 " pdb=" CA VAL D 119 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" CB ILE A 356 " pdb=" CG2 ILE A 356 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.06e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 14692 3.11 - 6.22: 365 6.22 - 9.33: 29 9.33 - 12.44: 4 12.44 - 15.55: 1 Bond angle restraints: 15091 Sorted by residual: angle pdb=" N PRO D 123 " pdb=" CA PRO D 123 " pdb=" C PRO D 123 " ideal model delta sigma weight residual 110.70 117.59 -6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 123.60 -9.70 1.80e+00 3.09e-01 2.91e+01 angle pdb=" C THR B 218 " pdb=" N ASP B 219 " pdb=" CA ASP B 219 " ideal model delta sigma weight residual 122.83 128.51 -5.68 1.08e+00 8.57e-01 2.76e+01 angle pdb=" CB MET B 267 " pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 112.70 97.15 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C THR C 237 " pdb=" N SER C 238 " pdb=" CA SER C 238 " ideal model delta sigma weight residual 121.70 130.89 -9.19 1.80e+00 3.09e-01 2.61e+01 ... (remaining 15086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6390 17.73 - 35.46: 244 35.46 - 53.19: 62 53.19 - 70.92: 5 70.92 - 88.65: 4 Dihedral angle restraints: 6705 sinusoidal: 2653 harmonic: 4052 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -174.65 88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CA GLY C 53 " pdb=" C GLY C 53 " pdb=" N SER C 54 " pdb=" CA SER C 54 " ideal model delta harmonic sigma weight residual -180.00 -140.63 -39.37 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1279 0.075 - 0.149: 356 0.149 - 0.224: 37 0.224 - 0.298: 8 0.298 - 0.373: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CB ILE B 444 " pdb=" CA ILE B 444 " pdb=" CG1 ILE B 444 " pdb=" CG2 ILE B 444 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB ILE A 444 " pdb=" CA ILE A 444 " pdb=" CG1 ILE A 444 " pdb=" CG2 ILE A 444 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1679 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 292 " -0.029 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 292 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 292 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 292 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 292 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 292 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 292 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 168 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C PHE B 168 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE B 168 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 169 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " -0.019 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " -0.000 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 476 2.69 - 3.24: 10072 3.24 - 3.80: 18651 3.80 - 4.35: 23532 4.35 - 4.90: 39709 Nonbonded interactions: 92440 Sorted by model distance: nonbonded pdb=" CB ALA D 115 " pdb=" N TYR D 144 " model vdw 2.138 3.540 nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 528 " pdb=" O THR A 531 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 205 " pdb=" OH TYR A 231 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 298 " pdb=" O GLY B 301 " model vdw 2.261 3.040 ... (remaining 92435 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' and resid 132 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.690 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.230 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.014 0.118 11078 Z= 0.947 Angle : 1.171 15.554 15091 Z= 0.659 Chirality : 0.067 0.373 1682 Planarity : 0.008 0.068 1953 Dihedral : 10.350 79.053 4057 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 0.57 % Allowed : 2.44 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.15 % 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: -3.08 (0.20), residues: 1387 helix: -1.99 (0.50), residues: 66 sheet: -1.94 (0.22), residues: 476 loop : -2.15 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP B 519 HIS 0.013 0.002 HIS A 233 PHE 0.057 0.006 PHE B 364 TYR 0.060 0.005 TYR B 292 ARG 0.014 0.002 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ARG cc_start: 0.4668 (mtm-85) cc_final: 0.3794 (mtt-85) REVERT: D 97 HIS cc_start: 0.6829 (m90) cc_final: 0.6440 (m-70) REVERT: D 212 PRO cc_start: 0.4885 (Cg_endo) cc_final: 0.4684 (Cg_exo) REVERT: C 34 MET cc_start: 0.6443 (mmm) cc_final: 0.5865 (mmm) REVERT: C 39 GLN cc_start: 0.5983 (tt0) cc_final: 0.5643 (tt0) REVERT: C 93 VAL cc_start: 0.6082 (t) cc_final: 0.5814 (p) REVERT: C 197 SER cc_start: 0.6115 (m) cc_final: 0.5707 (t) REVERT: A 381 ASN cc_start: 0.8349 (m-40) cc_final: 0.7991 (m-40) REVERT: A 391 LYS cc_start: 0.7348 (mtmt) cc_final: 0.6985 (ptpp) REVERT: A 425 LYS cc_start: 0.7135 (pttt) cc_final: 0.6869 (ptpp) REVERT: A 437 SER cc_start: 0.7316 (p) cc_final: 0.6947 (m) REVERT: A 501 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5945 (mm-30) REVERT: A 554 GLU cc_start: 0.6248 (tt0) cc_final: 0.5647 (tm-30) REVERT: A 589 ARG cc_start: 0.5795 (mtm180) cc_final: 0.4935 (mtp85) REVERT: B 199 LYS cc_start: 0.8082 (mttt) cc_final: 0.7678 (mmtp) REVERT: B 254 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6777 (mp0) REVERT: B 374 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 388 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6607 (tm-30) REVERT: B 389 TYR cc_start: 0.7984 (m-10) cc_final: 0.7295 (m-80) REVERT: B 399 MET cc_start: 0.7924 (mmm) cc_final: 0.7581 (mmm) REVERT: B 519 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6391 (t60) REVERT: B 527 ASP cc_start: 0.6327 (t70) cc_final: 0.6066 (t0) REVERT: B 550 GLN cc_start: 0.6973 (pt0) cc_final: 0.6334 (tt0) REVERT: B 569 LYS cc_start: 0.6103 (mtmm) cc_final: 0.5503 (mptt) REVERT: B 588 ILE cc_start: 0.7546 (mt) cc_final: 0.7099 (tp) REVERT: B 599 GLU cc_start: 0.6789 (mp0) cc_final: 0.6512 (tt0) outliers start: 7 outliers final: 5 residues processed: 214 average time/residue: 1.0920 time to fit residues: 254.7731 Evaluate side-chains 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN D 39 GLN C 82 GLN C 123 GLN C 189 GLN A 139 ASN A 159 ASN A 164 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 269 ASN A 287 ASN A 306 ASN A 333 HIS A 406 HIS A 423 ASN A 434 GLN A 529 ASN A 557 ASN B 141 ASN B 156 HIS B 195 ASN B 277 ASN B 406 HIS B 478 ASN B 530 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11078 Z= 0.268 Angle : 0.665 8.703 15091 Z= 0.352 Chirality : 0.048 0.237 1682 Planarity : 0.006 0.046 1953 Dihedral : 6.633 56.849 1521 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.71 % Allowed : 8.37 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.41 (0.21), residues: 1387 helix: -0.99 (0.57), residues: 67 sheet: -1.49 (0.23), residues: 471 loop : -1.74 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 519 HIS 0.005 0.001 HIS B 233 PHE 0.023 0.003 PHE C 184 TYR 0.028 0.002 TYR A 351 ARG 0.005 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7200 (m-80) cc_final: 0.6355 (m-80) REVERT: D 55 ARG cc_start: 0.4615 (mtm-85) cc_final: 0.4006 (mtt90) REVERT: D 97 HIS cc_start: 0.6406 (m90) cc_final: 0.6039 (m-70) REVERT: C 30 SER cc_start: 0.5382 (p) cc_final: 0.4855 (t) REVERT: C 34 MET cc_start: 0.6392 (mmm) cc_final: 0.5949 (mmm) REVERT: C 177 LEU cc_start: 0.3517 (tm) cc_final: 0.2851 (mm) REVERT: A 236 ARG cc_start: 0.5633 (ttt180) cc_final: 0.5283 (ttm170) REVERT: A 378 ASN cc_start: 0.6951 (t0) cc_final: 0.6612 (t0) REVERT: A 381 ASN cc_start: 0.8224 (m-40) cc_final: 0.7838 (m-40) REVERT: A 391 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6854 (pttm) REVERT: A 402 ARG cc_start: 0.7130 (ptt-90) cc_final: 0.6304 (mtm110) REVERT: A 425 LYS cc_start: 0.7113 (pttt) cc_final: 0.6684 (ptpp) REVERT: A 437 SER cc_start: 0.7519 (p) cc_final: 0.6820 (m) REVERT: A 501 GLU cc_start: 0.6112 (mm-30) cc_final: 0.5852 (mm-30) REVERT: A 554 GLU cc_start: 0.6277 (tt0) cc_final: 0.5672 (tm-30) REVERT: A 566 PHE cc_start: 0.6656 (p90) cc_final: 0.6425 (p90) REVERT: A 589 ARG cc_start: 0.5832 (mtm180) cc_final: 0.4960 (mtp85) REVERT: B 154 LYS cc_start: 0.6465 (mttt) cc_final: 0.6052 (mptt) REVERT: B 191 GLN cc_start: 0.7804 (mp10) cc_final: 0.6952 (mm-40) REVERT: B 199 LYS cc_start: 0.7996 (mttt) cc_final: 0.7731 (mmtp) REVERT: B 254 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6774 (mp0) REVERT: B 374 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6613 (mt-10) REVERT: B 388 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6633 (tm-30) REVERT: B 399 MET cc_start: 0.7785 (mmm) cc_final: 0.7315 (mmm) REVERT: B 519 TRP cc_start: 0.7247 (OUTLIER) cc_final: 0.4761 (t60) REVERT: B 527 ASP cc_start: 0.6308 (t70) cc_final: 0.5854 (t0) REVERT: B 550 GLN cc_start: 0.6823 (pt0) cc_final: 0.6444 (mt0) REVERT: B 559 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6746 (tp40) REVERT: B 569 LYS cc_start: 0.6106 (mtmm) cc_final: 0.5512 (mptt) REVERT: B 588 ILE cc_start: 0.7492 (mt) cc_final: 0.7127 (tp) REVERT: B 599 GLU cc_start: 0.6982 (mp0) cc_final: 0.6522 (tt0) outliers start: 21 outliers final: 7 residues processed: 170 average time/residue: 1.0039 time to fit residues: 188.1208 Evaluate side-chains 129 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 171 GLN C 77 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 388 GLN A 455 GLN A 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11078 Z= 0.301 Angle : 0.643 7.813 15091 Z= 0.337 Chirality : 0.049 0.265 1682 Planarity : 0.005 0.049 1953 Dihedral : 6.181 70.868 1516 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.92 % Allowed : 10.32 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.12 (0.21), residues: 1387 helix: 0.78 (0.71), residues: 54 sheet: -1.31 (0.22), residues: 490 loop : -1.64 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 479 HIS 0.005 0.001 HIS D 33 PHE 0.033 0.003 PHE B 290 TYR 0.034 0.002 TYR C 114 ARG 0.004 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.5913 (m-40) REVERT: D 37 TYR cc_start: 0.7262 (m-80) cc_final: 0.6408 (m-80) REVERT: D 55 ARG cc_start: 0.4467 (mtm-85) cc_final: 0.3776 (mtt90) REVERT: D 97 HIS cc_start: 0.6230 (m90) cc_final: 0.5560 (m90) REVERT: D 139 LEU cc_start: 0.5261 (mm) cc_final: 0.4980 (mm) REVERT: C 177 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.2829 (mm) REVERT: A 236 ARG cc_start: 0.5683 (ttt180) cc_final: 0.5321 (ttm170) REVERT: A 378 ASN cc_start: 0.7005 (t0) cc_final: 0.6684 (t0) REVERT: A 381 ASN cc_start: 0.8147 (m-40) cc_final: 0.7769 (m-40) REVERT: A 382 CYS cc_start: 0.5703 (t) cc_final: 0.5347 (t) REVERT: A 402 ARG cc_start: 0.7101 (ptt-90) cc_final: 0.6275 (mtm110) REVERT: A 420 ASP cc_start: 0.5639 (m-30) cc_final: 0.5266 (m-30) REVERT: A 425 LYS cc_start: 0.7159 (pttt) cc_final: 0.6773 (ptpp) REVERT: A 501 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5913 (mm-30) REVERT: A 554 GLU cc_start: 0.6307 (tt0) cc_final: 0.5705 (tm-30) REVERT: A 589 ARG cc_start: 0.5982 (mtm180) cc_final: 0.5001 (mtt90) REVERT: B 154 LYS cc_start: 0.6515 (mttt) cc_final: 0.6279 (mttp) REVERT: B 199 LYS cc_start: 0.8007 (mttt) cc_final: 0.7687 (mmtp) REVERT: B 217 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5727 (mm) REVERT: B 254 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6727 (mt-10) REVERT: B 374 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6599 (mt-10) REVERT: B 519 TRP cc_start: 0.7449 (OUTLIER) cc_final: 0.5445 (t60) REVERT: B 527 ASP cc_start: 0.6276 (t70) cc_final: 0.5903 (t0) REVERT: B 550 GLN cc_start: 0.6789 (pt0) cc_final: 0.6480 (mt0) REVERT: B 559 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6682 (tp-100) REVERT: B 569 LYS cc_start: 0.6086 (mtmm) cc_final: 0.5525 (mptt) REVERT: B 588 ILE cc_start: 0.7390 (mt) cc_final: 0.6918 (tp) REVERT: B 599 GLU cc_start: 0.7032 (mp0) cc_final: 0.6540 (tt0) outliers start: 36 outliers final: 15 residues processed: 163 average time/residue: 1.0451 time to fit residues: 187.8530 Evaluate side-chains 140 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.2980 chunk 94 optimal weight: 0.0770 chunk 65 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 192 HIS A 269 ASN A 543 ASN B 333 HIS B 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11078 Z= 0.206 Angle : 0.580 8.124 15091 Z= 0.302 Chirality : 0.047 0.177 1682 Planarity : 0.005 0.050 1953 Dihedral : 5.637 49.565 1516 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.17 % Allowed : 11.29 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.94 (0.22), residues: 1387 helix: 1.42 (0.74), residues: 54 sheet: -1.22 (0.22), residues: 498 loop : -1.52 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 121 HIS 0.007 0.001 HIS B 233 PHE 0.031 0.002 PHE B 229 TYR 0.032 0.002 TYR C 114 ARG 0.005 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7202 (m-80) cc_final: 0.6465 (m-80) REVERT: D 55 ARG cc_start: 0.4424 (mtm-85) cc_final: 0.3752 (mtt90) REVERT: D 97 HIS cc_start: 0.6095 (m90) cc_final: 0.5433 (m90) REVERT: C 49 SER cc_start: 0.7249 (p) cc_final: 0.6874 (t) REVERT: C 177 LEU cc_start: 0.3497 (OUTLIER) cc_final: 0.2917 (mm) REVERT: A 187 ASN cc_start: 0.6429 (t0) cc_final: 0.6213 (t0) REVERT: A 236 ARG cc_start: 0.5554 (ttt180) cc_final: 0.5200 (ttm170) REVERT: A 291 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: A 378 ASN cc_start: 0.7095 (t0) cc_final: 0.6862 (t0) REVERT: A 402 ARG cc_start: 0.7090 (ptt-90) cc_final: 0.6303 (mtm110) REVERT: A 420 ASP cc_start: 0.5682 (m-30) cc_final: 0.5417 (m-30) REVERT: A 425 LYS cc_start: 0.7057 (pttt) cc_final: 0.6676 (ptpp) REVERT: A 446 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: A 554 GLU cc_start: 0.6254 (tt0) cc_final: 0.5696 (tm-30) REVERT: A 566 PHE cc_start: 0.6575 (p90) cc_final: 0.6352 (p90) REVERT: A 589 ARG cc_start: 0.5862 (mtm180) cc_final: 0.4941 (mtt90) REVERT: B 154 LYS cc_start: 0.6473 (mttt) cc_final: 0.6248 (mttp) REVERT: B 199 LYS cc_start: 0.7994 (mttt) cc_final: 0.7702 (mmtp) REVERT: B 217 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5535 (mm) REVERT: B 254 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6773 (mp0) REVERT: B 360 ASP cc_start: 0.6320 (p0) cc_final: 0.6035 (p0) REVERT: B 399 MET cc_start: 0.7586 (mmm) cc_final: 0.7298 (mmm) REVERT: B 480 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6902 (mmm160) REVERT: B 519 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.4942 (t60) REVERT: B 527 ASP cc_start: 0.6298 (t70) cc_final: 0.5916 (t0) REVERT: B 550 GLN cc_start: 0.6686 (pt0) cc_final: 0.6476 (mt0) REVERT: B 559 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6692 (tp-100) REVERT: B 569 LYS cc_start: 0.5969 (mtmm) cc_final: 0.5376 (mptt) REVERT: B 588 ILE cc_start: 0.7325 (mt) cc_final: 0.6861 (tp) REVERT: B 599 GLU cc_start: 0.7058 (mp0) cc_final: 0.6522 (tt0) outliers start: 39 outliers final: 17 residues processed: 155 average time/residue: 0.9481 time to fit residues: 162.8903 Evaluate side-chains 137 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 559 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.0770 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN C 189 GLN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 509 ASN B 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11078 Z= 0.286 Angle : 0.609 8.825 15091 Z= 0.315 Chirality : 0.048 0.161 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.519 43.430 1516 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.09 % Allowed : 12.27 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.79 (0.22), residues: 1387 helix: 1.74 (0.76), residues: 54 sheet: -1.01 (0.23), residues: 489 loop : -1.52 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 519 HIS 0.005 0.001 HIS B 233 PHE 0.046 0.003 PHE D 143 TYR 0.028 0.002 TYR C 114 ARG 0.004 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7297 (m-80) cc_final: 0.6620 (m-80) REVERT: D 55 ARG cc_start: 0.4406 (mtm-85) cc_final: 0.3663 (mtt90) REVERT: D 97 HIS cc_start: 0.5961 (m90) cc_final: 0.5360 (m90) REVERT: D 139 LEU cc_start: 0.5174 (mm) cc_final: 0.4777 (mm) REVERT: C 177 LEU cc_start: 0.3482 (OUTLIER) cc_final: 0.2853 (mm) REVERT: A 187 ASN cc_start: 0.6367 (t0) cc_final: 0.6162 (t0) REVERT: A 236 ARG cc_start: 0.5656 (ttt180) cc_final: 0.5377 (ttm170) REVERT: A 378 ASN cc_start: 0.7207 (t0) cc_final: 0.6892 (t0) REVERT: A 402 ARG cc_start: 0.7087 (ptt-90) cc_final: 0.6252 (mtm110) REVERT: A 425 LYS cc_start: 0.6969 (pttt) cc_final: 0.6641 (ptpp) REVERT: A 446 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 554 GLU cc_start: 0.6262 (tt0) cc_final: 0.5644 (tm-30) REVERT: A 566 PHE cc_start: 0.6642 (p90) cc_final: 0.6412 (p90) REVERT: A 589 ARG cc_start: 0.6005 (mtm180) cc_final: 0.4997 (mtt90) REVERT: B 154 LYS cc_start: 0.6523 (mttt) cc_final: 0.6301 (mttp) REVERT: B 199 LYS cc_start: 0.8034 (mttt) cc_final: 0.7689 (mmtp) REVERT: B 217 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5782 (mm) REVERT: B 254 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6743 (mt-10) REVERT: B 360 ASP cc_start: 0.6493 (p0) cc_final: 0.6266 (p0) REVERT: B 519 TRP cc_start: 0.7550 (OUTLIER) cc_final: 0.5257 (t60) REVERT: B 527 ASP cc_start: 0.6325 (t70) cc_final: 0.5915 (t0) REVERT: B 550 GLN cc_start: 0.6658 (pt0) cc_final: 0.6405 (mt0) REVERT: B 569 LYS cc_start: 0.6123 (mtmm) cc_final: 0.5595 (mptt) REVERT: B 588 ILE cc_start: 0.7370 (mt) cc_final: 0.6858 (tp) REVERT: B 599 GLU cc_start: 0.7034 (mp0) cc_final: 0.6432 (tt0) outliers start: 38 outliers final: 23 residues processed: 143 average time/residue: 0.9665 time to fit residues: 153.2955 Evaluate side-chains 130 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11078 Z= 0.228 Angle : 0.583 8.963 15091 Z= 0.299 Chirality : 0.047 0.155 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.315 43.374 1516 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.09 % Allowed : 12.67 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.68 (0.22), residues: 1387 helix: 1.53 (0.72), residues: 61 sheet: -0.94 (0.22), residues: 499 loop : -1.44 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 519 HIS 0.007 0.001 HIS B 233 PHE 0.035 0.002 PHE D 143 TYR 0.036 0.002 TYR C 114 ARG 0.004 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.5840 (m-40) REVERT: D 37 TYR cc_start: 0.7310 (m-80) cc_final: 0.6630 (m-80) REVERT: D 55 ARG cc_start: 0.4336 (mtm-85) cc_final: 0.3607 (mtt90) REVERT: D 97 HIS cc_start: 0.5835 (m90) cc_final: 0.5234 (m90) REVERT: C 177 LEU cc_start: 0.3597 (OUTLIER) cc_final: 0.2972 (mm) REVERT: A 236 ARG cc_start: 0.5637 (ttt180) cc_final: 0.5386 (ttm170) REVERT: A 378 ASN cc_start: 0.7262 (t0) cc_final: 0.6935 (t0) REVERT: A 382 CYS cc_start: 0.5631 (t) cc_final: 0.5283 (t) REVERT: A 402 ARG cc_start: 0.7079 (ptt-90) cc_final: 0.6252 (mtm110) REVERT: A 425 LYS cc_start: 0.6946 (pttt) cc_final: 0.6605 (ptpp) REVERT: A 430 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: A 446 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: A 554 GLU cc_start: 0.6254 (tt0) cc_final: 0.5638 (tm-30) REVERT: A 566 PHE cc_start: 0.6605 (p90) cc_final: 0.6368 (p90) REVERT: A 589 ARG cc_start: 0.5945 (mtm180) cc_final: 0.4970 (mtt90) REVERT: B 154 LYS cc_start: 0.6546 (mttt) cc_final: 0.6326 (mttp) REVERT: B 199 LYS cc_start: 0.8010 (mttt) cc_final: 0.7670 (mmtp) REVERT: B 217 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5815 (mm) REVERT: B 254 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6755 (mp0) REVERT: B 360 ASP cc_start: 0.6475 (p0) cc_final: 0.6247 (p0) REVERT: B 519 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.5155 (t60) REVERT: B 527 ASP cc_start: 0.6338 (t70) cc_final: 0.5947 (t0) REVERT: B 550 GLN cc_start: 0.6624 (pt0) cc_final: 0.6366 (mt0) REVERT: B 588 ILE cc_start: 0.7355 (mt) cc_final: 0.6810 (tp) outliers start: 38 outliers final: 21 residues processed: 144 average time/residue: 0.8753 time to fit residues: 140.9839 Evaluate side-chains 129 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.0570 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 74 optimal weight: 0.0270 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN B 509 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11078 Z= 0.187 Angle : 0.570 8.941 15091 Z= 0.291 Chirality : 0.046 0.167 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.139 42.997 1516 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.09 % Allowed : 12.84 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.57 (0.22), residues: 1387 helix: 1.77 (0.73), residues: 61 sheet: -0.87 (0.22), residues: 495 loop : -1.38 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 310 HIS 0.014 0.001 HIS D 33 PHE 0.032 0.002 PHE D 143 TYR 0.030 0.002 TYR C 114 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7287 (m-80) cc_final: 0.6566 (m-80) REVERT: D 55 ARG cc_start: 0.4310 (mtm-85) cc_final: 0.3579 (mtt90) REVERT: D 97 HIS cc_start: 0.5700 (m90) cc_final: 0.5100 (m90) REVERT: C 128 THR cc_start: 0.6613 (m) cc_final: 0.6168 (p) REVERT: C 177 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.3010 (mm) REVERT: A 378 ASN cc_start: 0.7266 (t0) cc_final: 0.6943 (t0) REVERT: A 382 CYS cc_start: 0.5647 (t) cc_final: 0.5312 (t) REVERT: A 402 ARG cc_start: 0.7090 (ptt-90) cc_final: 0.6388 (mtm110) REVERT: A 425 LYS cc_start: 0.6840 (pttt) cc_final: 0.6572 (ptpp) REVERT: A 430 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 446 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: A 554 GLU cc_start: 0.6221 (tt0) cc_final: 0.5642 (tm-30) REVERT: A 566 PHE cc_start: 0.6714 (p90) cc_final: 0.6507 (p90) REVERT: A 589 ARG cc_start: 0.5756 (mtm180) cc_final: 0.4865 (mtt90) REVERT: B 191 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: B 199 LYS cc_start: 0.7921 (mttt) cc_final: 0.7615 (mmtp) REVERT: B 217 ILE cc_start: 0.6082 (OUTLIER) cc_final: 0.5685 (mm) REVERT: B 254 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6778 (mp0) REVERT: B 331 ASN cc_start: 0.5489 (m-40) cc_final: 0.5129 (t0) REVERT: B 388 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7131 (pp30) REVERT: B 399 MET cc_start: 0.7610 (mmm) cc_final: 0.7284 (mmm) REVERT: B 519 TRP cc_start: 0.7427 (OUTLIER) cc_final: 0.4939 (t60) REVERT: B 527 ASP cc_start: 0.6317 (t70) cc_final: 0.5931 (t0) REVERT: B 550 GLN cc_start: 0.6559 (pt0) cc_final: 0.6359 (mt0) REVERT: B 588 ILE cc_start: 0.7397 (mt) cc_final: 0.6860 (tp) outliers start: 38 outliers final: 23 residues processed: 142 average time/residue: 0.9329 time to fit residues: 147.9070 Evaluate side-chains 135 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN A 156 HIS A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11078 Z= 0.252 Angle : 0.598 9.076 15091 Z= 0.303 Chirality : 0.047 0.161 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.158 43.828 1515 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.01 % Allowed : 13.65 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.53 (0.22), residues: 1387 helix: 1.75 (0.73), residues: 61 sheet: -0.81 (0.23), residues: 491 loop : -1.37 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 310 HIS 0.006 0.001 HIS B 233 PHE 0.031 0.002 PHE B 290 TYR 0.030 0.002 TYR C 114 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7307 (m-80) cc_final: 0.6640 (m-80) REVERT: D 55 ARG cc_start: 0.4359 (mtm-85) cc_final: 0.3610 (mtt90) REVERT: D 97 HIS cc_start: 0.5674 (m90) cc_final: 0.5093 (m90) REVERT: C 49 SER cc_start: 0.7377 (p) cc_final: 0.6976 (t) REVERT: C 128 THR cc_start: 0.6563 (m) cc_final: 0.6114 (p) REVERT: C 177 LEU cc_start: 0.3667 (OUTLIER) cc_final: 0.3057 (mm) REVERT: A 236 ARG cc_start: 0.5734 (mtt180) cc_final: 0.5308 (ttm170) REVERT: A 378 ASN cc_start: 0.7280 (t0) cc_final: 0.6949 (t0) REVERT: A 382 CYS cc_start: 0.5603 (t) cc_final: 0.5301 (t) REVERT: A 402 ARG cc_start: 0.7097 (ptt-90) cc_final: 0.6270 (mtm110) REVERT: A 425 LYS cc_start: 0.6836 (pttt) cc_final: 0.6585 (ptpp) REVERT: A 430 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 554 GLU cc_start: 0.6236 (tt0) cc_final: 0.5625 (tm-30) REVERT: A 589 ARG cc_start: 0.5828 (mtm180) cc_final: 0.4899 (mtt90) REVERT: B 199 LYS cc_start: 0.7995 (mttt) cc_final: 0.7633 (mmtp) REVERT: B 217 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5638 (mm) REVERT: B 254 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6784 (mp0) REVERT: B 331 ASN cc_start: 0.5707 (m-40) cc_final: 0.5330 (t0) REVERT: B 519 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.5294 (t60) REVERT: B 527 ASP cc_start: 0.6320 (t70) cc_final: 0.5904 (t0) REVERT: B 550 GLN cc_start: 0.6646 (pt0) cc_final: 0.6418 (mt0) REVERT: B 588 ILE cc_start: 0.7426 (mt) cc_final: 0.6883 (tp) outliers start: 37 outliers final: 24 residues processed: 132 average time/residue: 0.9858 time to fit residues: 145.3629 Evaluate side-chains 127 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 1 GLN C 77 ASN A 156 HIS A 195 ASN A 492 GLN B 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11078 Z= 0.269 Angle : 0.606 8.780 15091 Z= 0.308 Chirality : 0.047 0.161 1682 Planarity : 0.005 0.052 1953 Dihedral : 5.207 44.077 1515 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.60 % Allowed : 13.97 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.48 (0.22), residues: 1387 helix: 1.79 (0.73), residues: 61 sheet: -0.73 (0.23), residues: 487 loop : -1.37 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 310 HIS 0.004 0.001 HIS B 233 PHE 0.031 0.002 PHE B 290 TYR 0.031 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7330 (m-80) cc_final: 0.6648 (m-80) REVERT: D 55 ARG cc_start: 0.4368 (mtm-85) cc_final: 0.3608 (mtt90) REVERT: D 97 HIS cc_start: 0.5645 (m90) cc_final: 0.5089 (m90) REVERT: C 128 THR cc_start: 0.6574 (m) cc_final: 0.6129 (p) REVERT: C 177 LEU cc_start: 0.3813 (OUTLIER) cc_final: 0.3155 (mm) REVERT: A 236 ARG cc_start: 0.5729 (mtt180) cc_final: 0.5301 (ttm170) REVERT: A 378 ASN cc_start: 0.7277 (t0) cc_final: 0.6947 (t0) REVERT: A 382 CYS cc_start: 0.5560 (t) cc_final: 0.5297 (t) REVERT: A 402 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6274 (mtm110) REVERT: A 425 LYS cc_start: 0.6846 (pttt) cc_final: 0.6588 (ptpp) REVERT: A 430 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 530 GLN cc_start: 0.6573 (mm-40) cc_final: 0.5946 (mm-40) REVERT: A 554 GLU cc_start: 0.6269 (tt0) cc_final: 0.5654 (tm-30) REVERT: A 589 ARG cc_start: 0.5884 (mtm180) cc_final: 0.4906 (mtt90) REVERT: B 199 LYS cc_start: 0.8044 (mttt) cc_final: 0.7667 (mmtp) REVERT: B 331 ASN cc_start: 0.5825 (m-40) cc_final: 0.5399 (t0) REVERT: B 388 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: B 399 MET cc_start: 0.7664 (mmm) cc_final: 0.7149 (mmm) REVERT: B 519 TRP cc_start: 0.7505 (OUTLIER) cc_final: 0.5413 (t60) REVERT: B 527 ASP cc_start: 0.6335 (t70) cc_final: 0.5926 (t0) REVERT: B 550 GLN cc_start: 0.6686 (pt0) cc_final: 0.6395 (mt0) REVERT: B 588 ILE cc_start: 0.7448 (mt) cc_final: 0.6939 (tp) outliers start: 32 outliers final: 23 residues processed: 133 average time/residue: 0.9112 time to fit residues: 135.2490 Evaluate side-chains 123 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.0010 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 195 ASN B 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11078 Z= 0.211 Angle : 0.583 8.753 15091 Z= 0.295 Chirality : 0.046 0.154 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.121 43.548 1515 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.27 % Allowed : 14.62 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.39 (0.22), residues: 1387 helix: 1.88 (0.74), residues: 61 sheet: -0.63 (0.23), residues: 483 loop : -1.33 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 310 HIS 0.008 0.001 HIS B 233 PHE 0.029 0.002 PHE B 290 TYR 0.031 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7292 (m-80) cc_final: 0.6645 (m-80) REVERT: D 55 ARG cc_start: 0.4332 (mtm-85) cc_final: 0.3584 (mtt90) REVERT: D 97 HIS cc_start: 0.5594 (m90) cc_final: 0.5040 (m90) REVERT: C 49 SER cc_start: 0.7335 (p) cc_final: 0.6954 (t) REVERT: C 128 THR cc_start: 0.6572 (m) cc_final: 0.6154 (p) REVERT: C 177 LEU cc_start: 0.3933 (OUTLIER) cc_final: 0.3297 (mm) REVERT: A 236 ARG cc_start: 0.5635 (mtt180) cc_final: 0.5211 (ttm170) REVERT: A 378 ASN cc_start: 0.7264 (t0) cc_final: 0.6938 (t0) REVERT: A 402 ARG cc_start: 0.7042 (ptt-90) cc_final: 0.6365 (mtm110) REVERT: A 430 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 530 GLN cc_start: 0.6495 (mm-40) cc_final: 0.5884 (mm-40) REVERT: A 554 GLU cc_start: 0.6248 (tt0) cc_final: 0.5617 (tm-30) REVERT: A 589 ARG cc_start: 0.5926 (mtm180) cc_final: 0.4941 (mtt90) REVERT: B 199 LYS cc_start: 0.8009 (mttt) cc_final: 0.7639 (mmtp) REVERT: B 324 LYS cc_start: 0.6256 (mmtm) cc_final: 0.5567 (mtmt) REVERT: B 331 ASN cc_start: 0.5689 (m-40) cc_final: 0.5273 (t0) REVERT: B 388 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7194 (pp30) REVERT: B 519 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.5188 (t60) REVERT: B 527 ASP cc_start: 0.6310 (t70) cc_final: 0.5915 (t0) REVERT: B 550 GLN cc_start: 0.6649 (pt0) cc_final: 0.6389 (mt0) REVERT: B 588 ILE cc_start: 0.7423 (mt) cc_final: 0.6920 (tp) outliers start: 28 outliers final: 22 residues processed: 130 average time/residue: 0.9175 time to fit residues: 133.2565 Evaluate side-chains 122 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.228935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183054 restraints weight = 11430.374| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 1.87 r_work: 0.4033 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11078 Z= 0.242 Angle : 0.591 8.996 15091 Z= 0.300 Chirality : 0.047 0.157 1682 Planarity : 0.005 0.050 1953 Dihedral : 5.148 43.791 1515 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.19 % Allowed : 15.27 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.33 (0.22), residues: 1387 helix: 1.90 (0.74), residues: 61 sheet: -0.55 (0.23), residues: 480 loop : -1.32 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 310 HIS 0.007 0.001 HIS B 233 PHE 0.030 0.002 PHE B 290 TYR 0.031 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4159.30 seconds wall clock time: 82 minutes 31.31 seconds (4951.31 seconds total)