Starting phenix.real_space_refine on Wed Sep 25 12:57:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/09_2024/7r89_24312.cif" } resolution = 2.6 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= 0.002 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 66 5.16 5 C 6811 2.51 5 N 1778 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4596 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 22, 'TRANS': 561} Chain breaks: 3 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4202 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.25, per 1000 atoms: 0.69 Number of scatterers: 10531 At special positions: 0 Unit cell: (116.48, 101.504, 123.968, 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 66 16.00 O 1876 8.00 N 1778 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 53.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.377A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.866A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 405 removed outlier: 5.475A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.054A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.993A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 removed outlier: 3.511A pdb=" N VAL A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.638A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.241A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.658A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 649 Proline residue: A 632 - end of helix Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.730A pdb=" N ARG B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 228 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 459 removed outlier: 4.638A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 490 through 517 removed outlier: 3.844A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix removed outlier: 4.042A pdb=" N TRP B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 594 through 609 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.804A pdb=" N MET B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.955A pdb=" N PHE C 51 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.663A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 6.624A pdb=" N LYS A 70 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER A 44 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 72 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 40 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR A 114 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS A 42 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A 112 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.354A pdb=" N MET A 214 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 248 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 216 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 273 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 267 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 96 removed outlier: 5.242A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 55 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 127 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96 removed outlier: 5.242A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.319A pdb=" N ALA B 149 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP B 237 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 151 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.133A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.348A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR D 69 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP D 55 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.348A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D 117 " --> pdb=" O GLN D 110 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1710 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: 3.41 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3342 1.35 - 1.46: 2562 1.46 - 1.58: 4752 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10761 Sorted by residual: bond pdb=" C10 ERG B 901 " pdb=" C9 ERG B 901 " ideal model delta sigma weight residual 1.556 1.507 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta sigma weight residual 1.459 1.473 -0.015 1.16e-02 7.43e+03 1.61e+00 bond pdb=" C10 ERG B 901 " pdb=" C5 ERG B 901 " ideal model delta sigma weight residual 1.519 1.496 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.14e+00 ... (remaining 10756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14277 1.58 - 3.15: 230 3.15 - 4.73: 39 4.73 - 6.30: 21 6.30 - 7.88: 4 Bond angle restraints: 14571 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.30 -2.97 8.00e-01 1.56e+00 1.38e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" CB VAL B 205 " ideal model delta sigma weight residual 112.39 108.80 3.59 1.17e+00 7.31e-01 9.42e+00 angle pdb=" C ARG C 63 " pdb=" CA ARG C 63 " pdb=" CB ARG C 63 " ideal model delta sigma weight residual 110.92 115.60 -4.68 1.59e+00 3.96e-01 8.66e+00 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 angle pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" C ILE B 459 " ideal model delta sigma weight residual 108.88 115.05 -6.17 2.16e+00 2.14e-01 8.16e+00 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5818 17.96 - 35.91: 460 35.91 - 53.86: 133 53.86 - 71.82: 30 71.82 - 89.77: 11 Dihedral angle restraints: 6452 sinusoidal: 2608 harmonic: 3844 Sorted by residual: dihedral pdb=" CB CYS A 587 " pdb=" SG CYS A 587 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual -86.00 -159.55 73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS D 43 " pdb=" SG CYS D 43 " pdb=" SG CYS D 108 " pdb=" CB CYS D 108 " ideal model delta sinusoidal sigma weight residual 93.00 65.05 27.95 1 1.00e+01 1.00e-02 1.12e+01 dihedral pdb=" CB GLU B 483 " pdb=" CG GLU B 483 " pdb=" CD GLU B 483 " pdb=" OE1 GLU B 483 " ideal model delta sinusoidal sigma weight residual 0.00 89.77 -89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1638 0.111 - 0.222: 22 0.222 - 0.334: 0 0.334 - 0.445: 1 0.445 - 0.556: 1 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C14 ERG B 901 " pdb=" C13 ERG B 901 " pdb=" C15 ERG B 901 " pdb=" C8 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.26 -2.82 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C10 ERG B 901 " pdb=" C1 ERG B 901 " pdb=" C5 ERG B 901 " pdb=" C9 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.77 -2.38 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C13 ERG B 901 " pdb=" C12 ERG B 901 " pdb=" C14 ERG B 901 " pdb=" C17 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1659 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 901 " 0.146 2.00e-02 2.50e+03 1.47e-01 2.15e+02 pdb=" C22 ERG B 901 " -0.141 2.00e-02 2.50e+03 pdb=" C23 ERG B 901 " -0.152 2.00e-02 2.50e+03 pdb=" C24 ERG B 901 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 513 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 514 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 277 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1396 2.76 - 3.29: 10098 3.29 - 3.83: 18206 3.83 - 4.36: 21016 4.36 - 4.90: 37151 Nonbonded interactions: 87867 Sorted by model distance: nonbonded pdb=" O ALA B 573 " pdb=" OG SER B 591 " model vdw 2.221 3.040 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 428 " pdb=" OG1 THR B 515 " model vdw 2.292 3.040 nonbonded pdb=" OG SER B 428 " pdb=" O TYR B 511 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 293 " pdb=" O ALA B 296 " model vdw 2.312 3.040 ... (remaining 87862 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 1.290 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.002 0.049 10761 Z= 0.133 Angle : 0.561 7.876 14571 Z= 0.318 Chirality : 0.041 0.556 1662 Planarity : 0.005 0.147 1828 Dihedral : 14.779 89.774 3975 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.39 % Allowed : 16.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.46 (0.22), residues: 1308 helix: 0.26 (0.19), residues: 681 sheet: -1.46 (0.33), residues: 178 loop : -2.63 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 55 HIS 0.003 0.001 HIS B 531 PHE 0.013 0.001 PHE B 493 TYR 0.008 0.001 TYR A 487 ARG 0.002 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8706 (tmm) cc_final: 0.8408 (tmm) REVERT: B 146 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8391 (tttm) REVERT: B 156 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: B 517 TRP cc_start: 0.7264 (m100) cc_final: 0.6768 (t60) REVERT: B 577 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5841 (mtp) outliers start: 39 outliers final: 14 residues processed: 255 average time/residue: 1.1582 time to fit residues: 318.4073 Evaluate side-chains 167 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 378 ASN A 425 GLN A 459 GLN A 462 GLN A 493 HIS A 578 ASN B 99 GLN B 155 ASN B 199 GLN B 249 HIS B 271 GLN B 302 GLN B 409 ASN B 438 HIS B 568 ASN C 58 GLN C 75 ASN C 103 GLN D 26 GLN D 47 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10761 Z= 0.237 Angle : 0.588 6.893 14571 Z= 0.299 Chirality : 0.041 0.144 1662 Planarity : 0.004 0.052 1828 Dihedral : 6.065 57.110 1549 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.95 % Allowed : 19.18 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1308 helix: 1.27 (0.20), residues: 685 sheet: -1.05 (0.35), residues: 182 loop : -1.79 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 584 HIS 0.006 0.001 HIS B 249 PHE 0.018 0.002 PHE B 595 TYR 0.017 0.002 TYR A 628 ARG 0.006 0.001 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8993 (tmm) cc_final: 0.8717 (tmm) REVERT: B 100 MET cc_start: 0.8888 (ttp) cc_final: 0.8679 (ttp) REVERT: B 392 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: B 474 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 517 TRP cc_start: 0.7369 (m100) cc_final: 0.6983 (t60) REVERT: C 26 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8635 (m) REVERT: C 103 GLN cc_start: 0.8495 (tp40) cc_final: 0.8173 (tp40) REVERT: D 90 ASP cc_start: 0.8539 (m-30) cc_final: 0.8283 (m-30) REVERT: D 125 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7994 (mt-10) outliers start: 57 outliers final: 21 residues processed: 194 average time/residue: 1.1697 time to fit residues: 246.9073 Evaluate side-chains 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 410 ASN A 425 GLN B 270 HIS B 607 GLN D 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10761 Z= 0.230 Angle : 0.577 8.411 14571 Z= 0.291 Chirality : 0.041 0.144 1662 Planarity : 0.004 0.055 1828 Dihedral : 5.044 55.919 1533 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.25 % Allowed : 20.05 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.37 (0.24), residues: 1308 helix: 1.63 (0.20), residues: 687 sheet: -0.69 (0.36), residues: 188 loop : -1.58 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 598 HIS 0.004 0.001 HIS A 510 PHE 0.016 0.001 PHE B 493 TYR 0.016 0.001 TYR A 114 ARG 0.003 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8099 (mm) cc_final: 0.7843 (mt) REVERT: A 425 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8268 (mp-120) REVERT: A 435 MET cc_start: 0.8944 (tmm) cc_final: 0.8689 (tmm) REVERT: B 100 MET cc_start: 0.8833 (ttp) cc_final: 0.8600 (ttp) REVERT: B 429 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7204 (mpt) REVERT: B 458 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 474 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 517 TRP cc_start: 0.7416 (m100) cc_final: 0.7008 (t60) REVERT: B 582 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7194 (p) REVERT: C 26 SER cc_start: 0.8907 (t) cc_final: 0.8639 (m) REVERT: C 99 ILE cc_start: 0.9076 (mt) cc_final: 0.8662 (mp) REVERT: C 103 GLN cc_start: 0.8424 (tp40) cc_final: 0.7789 (tp-100) REVERT: C 130 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: D 125 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7983 (mt-10) outliers start: 49 outliers final: 22 residues processed: 181 average time/residue: 1.1421 time to fit residues: 223.8243 Evaluate side-chains 162 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10761 Z= 0.190 Angle : 0.555 7.407 14571 Z= 0.280 Chirality : 0.040 0.144 1662 Planarity : 0.004 0.056 1828 Dihedral : 4.760 56.023 1530 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.95 % Allowed : 19.97 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.64 (0.24), residues: 1308 helix: 1.80 (0.20), residues: 687 sheet: -0.49 (0.37), residues: 188 loop : -1.42 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 598 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE B 493 TYR 0.016 0.001 TYR A 114 ARG 0.006 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 142 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8091 (mm) cc_final: 0.7848 (mt) REVERT: A 345 MET cc_start: 0.7545 (pp-130) cc_final: 0.7269 (tpp) REVERT: A 435 MET cc_start: 0.8939 (tmm) cc_final: 0.8716 (tmm) REVERT: A 647 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.6039 (t70) REVERT: B 100 MET cc_start: 0.8821 (ttp) cc_final: 0.8596 (ttp) REVERT: B 474 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 503 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 517 TRP cc_start: 0.7403 (m100) cc_final: 0.7002 (t60) REVERT: B 582 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7128 (p) REVERT: C 26 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8645 (m) REVERT: C 32 GLN cc_start: 0.6025 (OUTLIER) cc_final: 0.5793 (mm110) REVERT: C 88 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7437 (mtm-85) REVERT: C 99 ILE cc_start: 0.9079 (mt) cc_final: 0.8661 (mp) REVERT: C 103 GLN cc_start: 0.8507 (tp40) cc_final: 0.8080 (tp40) REVERT: D 125 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8010 (mt-10) outliers start: 57 outliers final: 25 residues processed: 186 average time/residue: 1.1697 time to fit residues: 235.5592 Evaluate side-chains 169 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10761 Z= 0.291 Angle : 0.607 8.758 14571 Z= 0.308 Chirality : 0.042 0.144 1662 Planarity : 0.004 0.056 1828 Dihedral : 4.908 50.230 1530 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.69 % Allowed : 19.79 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.66 (0.24), residues: 1308 helix: 1.75 (0.20), residues: 686 sheet: -0.38 (0.37), residues: 188 loop : -1.32 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 598 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.002 PHE B 493 TYR 0.017 0.002 TYR A 114 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8115 (mm) cc_final: 0.7868 (mt) REVERT: A 345 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7328 (tpp) REVERT: A 425 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8312 (mp-120) REVERT: A 599 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6014 (mmt) REVERT: A 647 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.6094 (t70) REVERT: B 100 MET cc_start: 0.8843 (ttp) cc_final: 0.8538 (ttp) REVERT: B 156 GLN cc_start: 0.7826 (pm20) cc_final: 0.7569 (pm20) REVERT: B 441 ILE cc_start: 0.9118 (mt) cc_final: 0.8831 (mm) REVERT: B 474 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 503 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: B 517 TRP cc_start: 0.7395 (m100) cc_final: 0.7019 (t60) REVERT: B 582 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7246 (p) REVERT: C 26 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8663 (m) REVERT: C 88 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: C 99 ILE cc_start: 0.9109 (mt) cc_final: 0.8694 (mp) REVERT: C 103 GLN cc_start: 0.8419 (tp40) cc_final: 0.7742 (tp-100) REVERT: C 123 MET cc_start: 0.8652 (mmp) cc_final: 0.8440 (mmm) REVERT: C 130 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: D 97 SER cc_start: 0.8113 (t) cc_final: 0.7861 (p) REVERT: D 125 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8040 (mt-10) outliers start: 54 outliers final: 31 residues processed: 178 average time/residue: 1.1564 time to fit residues: 222.5235 Evaluate side-chains 174 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10761 Z= 0.310 Angle : 0.614 8.582 14571 Z= 0.313 Chirality : 0.042 0.146 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.953 49.869 1530 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.69 % Allowed : 19.88 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.65 (0.24), residues: 1308 helix: 1.73 (0.20), residues: 684 sheet: -0.39 (0.38), residues: 188 loop : -1.29 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS A 510 PHE 0.018 0.002 PHE B 493 TYR 0.016 0.002 TYR A 114 ARG 0.008 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8111 (mm) cc_final: 0.7876 (mt) REVERT: A 345 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: A 599 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6188 (mmt) REVERT: A 647 HIS cc_start: 0.6400 (OUTLIER) cc_final: 0.6125 (t70) REVERT: B 26 ARG cc_start: 0.4662 (ptt180) cc_final: 0.4443 (ptt180) REVERT: B 121 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5745 (mmt-90) REVERT: B 156 GLN cc_start: 0.7807 (pm20) cc_final: 0.7558 (pm20) REVERT: B 441 ILE cc_start: 0.9119 (mt) cc_final: 0.8828 (mm) REVERT: B 474 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 503 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: B 517 TRP cc_start: 0.7412 (m100) cc_final: 0.7031 (t60) REVERT: B 582 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7282 (p) REVERT: C 26 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (m) REVERT: C 88 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7455 (mtm-85) REVERT: C 99 ILE cc_start: 0.9112 (mt) cc_final: 0.8705 (mp) REVERT: C 103 GLN cc_start: 0.8411 (tp40) cc_final: 0.7738 (tp-100) REVERT: D 97 SER cc_start: 0.8151 (t) cc_final: 0.7922 (p) REVERT: D 125 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7981 (mt-10) outliers start: 54 outliers final: 31 residues processed: 180 average time/residue: 1.2004 time to fit residues: 233.6356 Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10761 Z= 0.308 Angle : 0.620 8.844 14571 Z= 0.315 Chirality : 0.042 0.146 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.982 48.881 1530 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.60 % Allowed : 19.79 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.69 (0.24), residues: 1308 helix: 1.75 (0.20), residues: 683 sheet: -0.28 (0.39), residues: 178 loop : -1.26 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.002 PHE B 493 TYR 0.016 0.002 TYR A 114 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8114 (mm) cc_final: 0.7891 (mt) REVERT: A 345 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7350 (tpp) REVERT: A 425 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8301 (mp-120) REVERT: A 647 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.6105 (t70) REVERT: B 121 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.5685 (mmt-90) REVERT: B 156 GLN cc_start: 0.7807 (pm20) cc_final: 0.7517 (pm20) REVERT: B 474 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 503 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: B 517 TRP cc_start: 0.7402 (m100) cc_final: 0.7023 (t60) REVERT: B 582 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7253 (p) REVERT: C 26 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8642 (m) REVERT: C 88 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7461 (mtm-85) REVERT: C 99 ILE cc_start: 0.9114 (mt) cc_final: 0.8717 (mp) REVERT: C 103 GLN cc_start: 0.8403 (tp40) cc_final: 0.7721 (tp-100) REVERT: C 130 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: D 97 SER cc_start: 0.8221 (t) cc_final: 0.8019 (p) REVERT: D 125 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7963 (mt-10) outliers start: 53 outliers final: 31 residues processed: 175 average time/residue: 1.1871 time to fit residues: 224.1872 Evaluate side-chains 173 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10761 Z= 0.182 Angle : 0.564 8.000 14571 Z= 0.286 Chirality : 0.040 0.145 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.733 47.399 1530 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.82 % Allowed : 21.01 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.88 (0.24), residues: 1308 helix: 1.94 (0.20), residues: 683 sheet: -0.35 (0.39), residues: 183 loop : -1.18 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE B 493 TYR 0.018 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8080 (mm) cc_final: 0.7849 (mt) REVERT: A 345 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7318 (tpp) REVERT: A 529 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 647 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5991 (t70) REVERT: B 121 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5610 (mmt-90) REVERT: B 156 GLN cc_start: 0.7785 (pm20) cc_final: 0.7511 (pm20) REVERT: B 474 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7605 (mt-10) REVERT: B 503 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 517 TRP cc_start: 0.7410 (m100) cc_final: 0.7060 (t60) REVERT: B 582 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7151 (p) REVERT: C 26 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (m) REVERT: C 88 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7453 (mtm-85) REVERT: C 99 ILE cc_start: 0.9101 (mt) cc_final: 0.8703 (mp) REVERT: C 103 GLN cc_start: 0.8382 (tp40) cc_final: 0.7720 (tp-100) REVERT: D 125 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8009 (mt-10) outliers start: 44 outliers final: 26 residues processed: 173 average time/residue: 1.1738 time to fit residues: 219.2717 Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10761 Z= 0.194 Angle : 0.578 10.327 14571 Z= 0.290 Chirality : 0.040 0.143 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.564 47.250 1529 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.47 % Allowed : 21.70 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.98 (0.24), residues: 1308 helix: 2.00 (0.20), residues: 683 sheet: -0.15 (0.39), residues: 178 loop : -1.16 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8067 (mm) cc_final: 0.7848 (mt) REVERT: A 345 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7316 (tpp) REVERT: A 529 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 156 GLN cc_start: 0.7783 (pm20) cc_final: 0.7513 (pm20) REVERT: B 474 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 503 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: B 517 TRP cc_start: 0.7394 (m100) cc_final: 0.7030 (t60) REVERT: B 582 SER cc_start: 0.7386 (OUTLIER) cc_final: 0.7088 (p) REVERT: C 26 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8644 (m) REVERT: C 88 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7443 (mtm-85) REVERT: C 99 ILE cc_start: 0.9104 (mt) cc_final: 0.8690 (mp) REVERT: C 103 GLN cc_start: 0.8367 (tp40) cc_final: 0.7712 (tp-100) REVERT: D 125 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8004 (mt-10) outliers start: 40 outliers final: 25 residues processed: 166 average time/residue: 1.1648 time to fit residues: 208.9805 Evaluate side-chains 165 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 425 GLN B 607 GLN D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10761 Z= 0.257 Angle : 0.869 59.199 14571 Z= 0.490 Chirality : 0.042 0.373 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.515 47.302 1528 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.21 % Allowed : 21.96 % Favored : 74.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.66 % 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: 0.96 (0.24), residues: 1308 helix: 1.98 (0.20), residues: 683 sheet: -0.23 (0.38), residues: 188 loop : -1.13 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 493 TYR 0.015 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8070 (mm) cc_final: 0.7852 (mt) REVERT: A 345 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7319 (tpp) REVERT: A 529 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8817 (mp) REVERT: B 156 GLN cc_start: 0.7785 (pm20) cc_final: 0.7515 (pm20) REVERT: B 474 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 503 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 517 TRP cc_start: 0.7397 (m100) cc_final: 0.7035 (t60) REVERT: B 582 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7097 (p) REVERT: C 26 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 88 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7444 (mtm-85) REVERT: C 99 ILE cc_start: 0.9114 (mt) cc_final: 0.8693 (mp) REVERT: C 103 GLN cc_start: 0.8382 (tp40) cc_final: 0.7712 (tp-100) REVERT: D 125 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8006 (mt-10) outliers start: 37 outliers final: 26 residues processed: 163 average time/residue: 1.2373 time to fit residues: 218.1037 Evaluate side-chains 165 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.081612 restraints weight = 14139.363| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.12 r_work: 0.2795 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10761 Z= 0.257 Angle : 0.869 59.199 14571 Z= 0.490 Chirality : 0.042 0.373 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.515 47.302 1528 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.95 % Allowed : 22.05 % Favored : 75.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.66 % 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: 0.96 (0.24), residues: 1308 helix: 1.98 (0.20), residues: 683 sheet: -0.23 (0.38), residues: 188 loop : -1.13 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 493 TYR 0.015 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 =============================================================================== Job complete usr+sys time: 4398.36 seconds wall clock time: 77 minutes 25.13 seconds (4645.13 seconds total)