Starting phenix.real_space_refine on Mon Jul 28 13:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_24312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_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/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_24312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_24312.map" model { file = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_24312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2025/7r89_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-5711/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: 6.85, per 1000 atoms: 0.65 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.61 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: 3.60 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: 1.23 - 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: 1.960 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: 0.070 Set scattering table: 0.100 Process input model: 26.820 Find NCS groups from input model: 0.140 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- 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 10764 Z= 0.121 Angle : 0.563 7.876 14577 Z= 0.319 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 Details of bonding type rmsd hydrogen bonds : bond 0.12640 ( 591) hydrogen bonds : angle 5.27759 ( 1710) SS BOND : bond 0.00147 ( 3) SS BOND : angle 2.07155 ( 6) covalent geometry : bond 0.00211 (10761) covalent geometry : angle 0.56112 (14571) *********************** 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 to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 1.128 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: 1.2867 time to fit residues: 353.7001 Evaluate side-chains 167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 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 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: 8.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083822 restraints weight = 14289.239| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.18 r_work: 0.2827 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 10764 Z= 0.164 Angle : 0.588 6.893 14577 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 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 591) hydrogen bonds : angle 4.19690 ( 1710) SS BOND : bond 0.00646 ( 3) SS BOND : angle 0.91606 ( 6) covalent geometry : bond 0.00369 (10761) covalent geometry : angle 0.58792 (14571) *********************** 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 to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 411 VAL cc_start: 0.6532 (p) cc_final: 0.6294 (t) REVERT: A 435 MET cc_start: 0.9227 (tmm) cc_final: 0.8981 (tmm) REVERT: A 647 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6687 (t-90) REVERT: B 392 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: B 474 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 517 TRP cc_start: 0.7796 (m100) cc_final: 0.6990 (t60) REVERT: C 26 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8543 (m) REVERT: C 103 GLN cc_start: 0.8507 (tp40) cc_final: 0.8124 (tp40) REVERT: D 90 ASP cc_start: 0.8677 (m-30) cc_final: 0.8446 (m-30) REVERT: D 125 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8190 (mt-10) outliers start: 57 outliers final: 21 residues processed: 194 average time/residue: 1.2257 time to fit residues: 257.0394 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 A residue 647 HIS 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 117 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 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 392 GLN A 393 ASN A 425 GLN B 270 HIS B 607 GLN D 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.079773 restraints weight = 14464.787| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.19 r_work: 0.2756 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10764 Z= 0.207 Angle : 0.623 8.910 14577 Z= 0.315 Chirality : 0.043 0.146 1662 Planarity : 0.004 0.055 1828 Dihedral : 5.321 59.746 1533 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: 0.27 (0.23), residues: 1308 helix: 1.53 (0.20), residues: 686 sheet: -0.70 (0.36), residues: 188 loop : -1.62 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 598 HIS 0.005 0.001 HIS A 510 PHE 0.017 0.002 PHE B 493 TYR 0.016 0.002 TYR A 114 ARG 0.003 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 591) hydrogen bonds : angle 4.24235 ( 1710) SS BOND : bond 0.00426 ( 3) SS BOND : angle 1.11090 ( 6) covalent geometry : bond 0.00484 (10761) covalent geometry : angle 0.62306 (14571) *********************** 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 196 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8143 (mm) cc_final: 0.7887 (mt) REVERT: A 425 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8713 (mp-120) REVERT: A 599 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5968 (mtt) REVERT: B 392 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7523 (mpp) REVERT: B 458 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B 474 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 517 TRP cc_start: 0.7841 (m100) cc_final: 0.7033 (t60) REVERT: B 582 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7263 (p) REVERT: C 26 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8550 (m) REVERT: C 94 ASP cc_start: 0.8425 (t0) cc_final: 0.8173 (t0) REVERT: C 99 ILE cc_start: 0.8928 (mt) cc_final: 0.8501 (mp) REVERT: C 103 GLN cc_start: 0.8437 (tp40) cc_final: 0.7673 (tp-100) REVERT: C 130 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: D 125 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8214 (mt-10) outliers start: 57 outliers final: 29 residues processed: 182 average time/residue: 1.1981 time to fit residues: 236.6305 Evaluate side-chains 171 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 599 MET 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 244 ASP 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 325 THR Chi-restraints excluded: chain B residue 392 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 545 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 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 59 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081978 restraints weight = 14354.715| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.07 r_work: 0.2801 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10764 Z= 0.137 Angle : 0.565 7.832 14577 Z= 0.285 Chirality : 0.040 0.142 1662 Planarity : 0.004 0.057 1828 Dihedral : 5.020 55.818 1531 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.51 % Allowed : 19.36 % Favored : 76.13 % 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: 0.57 (0.24), residues: 1308 helix: 1.77 (0.20), residues: 685 sheet: -0.55 (0.37), residues: 188 loop : -1.45 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS A 510 PHE 0.016 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.006 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 591) hydrogen bonds : angle 4.12727 ( 1710) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.77258 ( 6) covalent geometry : bond 0.00303 (10761) covalent geometry : angle 0.56485 (14571) *********************** 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 191 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8061 (mm) cc_final: 0.7834 (mt) REVERT: A 345 MET cc_start: 0.7685 (pp-130) cc_final: 0.7167 (tpp) REVERT: A 411 VAL cc_start: 0.6556 (p) cc_final: 0.6314 (t) REVERT: A 599 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5608 (mmt) REVERT: B 392 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7522 (mpp) REVERT: B 441 ILE cc_start: 0.8995 (mt) cc_final: 0.8619 (mm) REVERT: B 474 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 503 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: B 517 TRP cc_start: 0.7780 (m100) cc_final: 0.6971 (t60) REVERT: B 582 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.7234 (p) REVERT: C 26 SER cc_start: 0.8897 (t) cc_final: 0.8515 (m) REVERT: C 32 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5857 (mm110) REVERT: C 88 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7742 (mtm-85) REVERT: C 94 ASP cc_start: 0.8377 (t0) cc_final: 0.8125 (t0) REVERT: C 99 ILE cc_start: 0.8861 (mt) cc_final: 0.8428 (mp) REVERT: C 103 GLN cc_start: 0.8508 (tp40) cc_final: 0.7985 (tp40) REVERT: C 123 MET cc_start: 0.9118 (mmp) cc_final: 0.8863 (mmm) REVERT: D 125 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8164 (mt-10) outliers start: 52 outliers final: 26 residues processed: 181 average time/residue: 1.4555 time to fit residues: 286.8425 Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 599 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 200 CYS 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 392 MET Chi-restraints excluded: chain B residue 429 MET 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 635 LEU 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 38 ARG 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 90 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.082566 restraints weight = 14730.794| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.13 r_work: 0.2824 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10764 Z= 0.146 Angle : 0.569 7.892 14577 Z= 0.288 Chirality : 0.040 0.143 1662 Planarity : 0.004 0.057 1828 Dihedral : 4.952 55.505 1531 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.69 % Allowed : 19.36 % Favored : 75.95 % 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: 0.74 (0.24), residues: 1308 helix: 1.86 (0.20), residues: 685 sheet: -0.43 (0.37), residues: 188 loop : -1.34 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS A 510 PHE 0.017 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.006 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 591) hydrogen bonds : angle 4.07417 ( 1710) SS BOND : bond 0.00331 ( 3) SS BOND : angle 0.80408 ( 6) covalent geometry : bond 0.00330 (10761) covalent geometry : angle 0.56891 (14571) *********************** 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 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8074 (mm) cc_final: 0.7846 (mt) REVERT: A 345 MET cc_start: 0.7682 (pp-130) cc_final: 0.7148 (tpp) REVERT: A 411 VAL cc_start: 0.6544 (p) cc_final: 0.6296 (t) REVERT: A 425 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8625 (mp-120) REVERT: A 599 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5701 (mmt) REVERT: B 156 GLN cc_start: 0.8095 (pm20) cc_final: 0.7813 (pm20) REVERT: B 392 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7542 (mpp) REVERT: B 441 ILE cc_start: 0.9021 (mt) cc_final: 0.8648 (mm) REVERT: B 474 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 503 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: B 517 TRP cc_start: 0.7822 (m100) cc_final: 0.6985 (t60) REVERT: B 582 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 26 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8498 (m) REVERT: C 88 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7735 (mtm-85) REVERT: C 94 ASP cc_start: 0.8330 (t0) cc_final: 0.8064 (t0) REVERT: C 99 ILE cc_start: 0.8877 (mt) cc_final: 0.8449 (mp) REVERT: C 103 GLN cc_start: 0.8383 (tp40) cc_final: 0.7569 (tp-100) REVERT: D 97 SER cc_start: 0.8205 (t) cc_final: 0.7934 (p) REVERT: D 125 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8146 (mt-10) outliers start: 54 outliers final: 29 residues processed: 182 average time/residue: 1.1969 time to fit residues: 235.8001 Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 351 LEU Chi-restraints excluded: chain A residue 353 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 550 ARG Chi-restraints excluded: chain A residue 599 MET 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 392 MET Chi-restraints excluded: chain B residue 458 LEU 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 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 94 THR 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 93 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080265 restraints weight = 14328.181| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.07 r_work: 0.2770 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10764 Z= 0.178 Angle : 0.592 8.219 14577 Z= 0.300 Chirality : 0.041 0.144 1662 Planarity : 0.004 0.057 1828 Dihedral : 4.819 50.271 1529 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.08 % Allowed : 20.40 % 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: 0.74 (0.24), residues: 1308 helix: 1.81 (0.20), residues: 685 sheet: -0.38 (0.38), residues: 188 loop : -1.27 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.002 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.005 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 591) hydrogen bonds : angle 4.13217 ( 1710) SS BOND : bond 0.00354 ( 3) SS BOND : angle 0.95550 ( 6) covalent geometry : bond 0.00414 (10761) covalent geometry : angle 0.59181 (14571) *********************** 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 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8083 (mm) cc_final: 0.7858 (mt) REVERT: A 345 MET cc_start: 0.7697 (pp-130) cc_final: 0.7170 (tpp) REVERT: A 411 VAL cc_start: 0.6507 (p) cc_final: 0.6253 (t) REVERT: A 599 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5794 (mmt) REVERT: A 647 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6476 (t-170) REVERT: B 156 GLN cc_start: 0.8068 (pm20) cc_final: 0.7798 (pm20) REVERT: B 392 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7547 (mpp) REVERT: B 441 ILE cc_start: 0.9029 (mt) cc_final: 0.8653 (mm) REVERT: B 474 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 503 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: B 517 TRP cc_start: 0.7781 (m100) cc_final: 0.6973 (t60) REVERT: B 582 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7223 (p) REVERT: C 26 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 88 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7684 (mtm-85) REVERT: C 94 ASP cc_start: 0.8356 (t0) cc_final: 0.8074 (t0) REVERT: C 99 ILE cc_start: 0.8889 (mt) cc_final: 0.8452 (mp) REVERT: C 103 GLN cc_start: 0.8401 (tp40) cc_final: 0.7559 (tp-100) REVERT: D 97 SER cc_start: 0.8235 (t) cc_final: 0.7984 (p) REVERT: D 125 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8184 (mt-10) outliers start: 47 outliers final: 30 residues processed: 177 average time/residue: 1.1476 time to fit residues: 220.3140 Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 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 392 MET Chi-restraints excluded: chain B residue 458 LEU 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 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 94 THR 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 73 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.080957 restraints weight = 14397.303| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.15 r_work: 0.2778 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10764 Z= 0.155 Angle : 0.578 7.932 14577 Z= 0.292 Chirality : 0.041 0.145 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.730 49.154 1529 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.34 % Allowed : 19.88 % Favored : 75.78 % 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: 0.83 (0.24), residues: 1308 helix: 1.90 (0.20), residues: 685 sheet: -0.37 (0.37), residues: 188 loop : -1.23 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS A 510 PHE 0.017 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 591) hydrogen bonds : angle 4.09303 ( 1710) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.89272 ( 6) covalent geometry : bond 0.00354 (10761) covalent geometry : angle 0.57801 (14571) *********************** 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 193 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8056 (mm) cc_final: 0.7840 (mt) REVERT: A 345 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: A 353 MET cc_start: 0.8075 (pmm) cc_final: 0.7439 (mmt) REVERT: A 411 VAL cc_start: 0.6425 (p) cc_final: 0.6198 (t) REVERT: A 529 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8770 (mp) REVERT: A 599 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5882 (mmt) REVERT: A 647 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.6437 (t-170) REVERT: B 26 ARG cc_start: 0.6343 (ptt180) cc_final: 0.6128 (ptt180) REVERT: B 121 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5623 (mmt-90) REVERT: B 156 GLN cc_start: 0.8065 (pm20) cc_final: 0.7744 (pm20) REVERT: B 392 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: B 474 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 503 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 517 TRP cc_start: 0.7764 (m100) cc_final: 0.6967 (t60) REVERT: B 582 SER cc_start: 0.7587 (OUTLIER) cc_final: 0.7182 (p) REVERT: C 26 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8504 (m) REVERT: C 88 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7648 (mtm-85) REVERT: C 94 ASP cc_start: 0.8341 (t0) cc_final: 0.8027 (t0) REVERT: C 99 ILE cc_start: 0.8888 (mt) cc_final: 0.8455 (mp) REVERT: C 103 GLN cc_start: 0.8392 (tp40) cc_final: 0.7573 (tp-100) REVERT: D 38 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7895 (ptm-80) REVERT: D 97 SER cc_start: 0.8260 (t) cc_final: 0.8013 (p) REVERT: D 125 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 50 outliers final: 31 residues processed: 179 average time/residue: 1.1416 time to fit residues: 221.2013 Evaluate side-chains 179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 366 SER 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 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 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 256 SER Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 458 LEU 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 38 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.080868 restraints weight = 14265.225| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.14 r_work: 0.2779 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10764 Z= 0.152 Angle : 0.581 8.127 14577 Z= 0.292 Chirality : 0.041 0.146 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.711 49.318 1529 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.43 % Allowed : 19.88 % 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: 0.86 (0.24), residues: 1308 helix: 1.92 (0.20), residues: 685 sheet: -0.32 (0.38), residues: 188 loop : -1.22 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 591) hydrogen bonds : angle 4.07925 ( 1710) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.86142 ( 6) covalent geometry : bond 0.00347 (10761) covalent geometry : angle 0.58055 (14571) *********************** 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 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8064 (mm) cc_final: 0.7848 (mt) REVERT: A 345 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7154 (tpp) REVERT: A 353 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: A 411 VAL cc_start: 0.6282 (p) cc_final: 0.6064 (t) REVERT: A 529 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 599 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5867 (mmt) REVERT: A 647 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6419 (t-170) REVERT: B 26 ARG cc_start: 0.6333 (ptt180) cc_final: 0.6121 (ptt180) REVERT: B 121 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.5618 (mmt-90) REVERT: B 156 GLN cc_start: 0.8057 (pm20) cc_final: 0.7743 (pm20) REVERT: B 392 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7476 (mpp) REVERT: B 474 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 503 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: B 517 TRP cc_start: 0.7778 (m100) cc_final: 0.6973 (t60) REVERT: B 582 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7180 (p) REVERT: C 26 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8518 (m) REVERT: C 88 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7631 (mtm-85) REVERT: C 94 ASP cc_start: 0.8357 (t0) cc_final: 0.8053 (t0) REVERT: C 99 ILE cc_start: 0.8893 (mt) cc_final: 0.8469 (mp) REVERT: C 103 GLN cc_start: 0.8382 (tp40) cc_final: 0.7545 (tp-100) REVERT: D 38 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7877 (ptm-80) REVERT: D 97 SER cc_start: 0.8273 (t) cc_final: 0.8020 (p) REVERT: D 125 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8081 (mt-10) outliers start: 51 outliers final: 31 residues processed: 174 average time/residue: 1.2123 time to fit residues: 227.2449 Evaluate side-chains 179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET 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 529 ILE 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 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 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 458 LEU 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 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 38 ARG 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 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.080998 restraints weight = 14332.774| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.14 r_work: 0.2781 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10764 Z= 0.150 Angle : 0.584 8.585 14577 Z= 0.293 Chirality : 0.041 0.145 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.677 48.847 1529 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.51 % Allowed : 19.97 % 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: 0.91 (0.24), residues: 1308 helix: 1.95 (0.20), residues: 685 sheet: -0.29 (0.38), residues: 188 loop : -1.18 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE B 493 TYR 0.017 0.001 TYR A 114 ARG 0.010 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 591) hydrogen bonds : angle 4.06720 ( 1710) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.83611 ( 6) covalent geometry : bond 0.00342 (10761) covalent geometry : angle 0.58396 (14571) *********************** 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 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8066 (mm) cc_final: 0.7849 (mt) REVERT: A 345 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: A 353 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: A 406 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7977 (mtt180) REVERT: A 529 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 647 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.6352 (t-170) REVERT: B 26 ARG cc_start: 0.6351 (ptt180) cc_final: 0.6133 (ptt180) REVERT: B 121 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5613 (mmt-90) REVERT: B 156 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: B 392 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7461 (mpp) REVERT: B 474 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 503 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 517 TRP cc_start: 0.7804 (m100) cc_final: 0.6997 (t60) REVERT: B 582 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7161 (p) REVERT: C 26 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8514 (m) REVERT: C 88 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7608 (mtm-85) REVERT: C 94 ASP cc_start: 0.8311 (t0) cc_final: 0.8010 (t0) REVERT: C 99 ILE cc_start: 0.8887 (mt) cc_final: 0.8465 (mp) REVERT: C 103 GLN cc_start: 0.8374 (tp40) cc_final: 0.7533 (tp-100) REVERT: D 38 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7856 (ptm-80) REVERT: D 97 SER cc_start: 0.8286 (t) cc_final: 0.8036 (p) REVERT: D 125 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8079 (mt-10) outliers start: 52 outliers final: 29 residues processed: 174 average time/residue: 1.2439 time to fit residues: 233.8794 Evaluate side-chains 180 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 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 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 406 ARG 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 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 156 GLN 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 392 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 560 SER 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 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG 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 126 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.080992 restraints weight = 14303.979| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.07 r_work: 0.2788 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10764 Z= 0.163 Angle : 0.857 59.194 14577 Z= 0.482 Chirality : 0.041 0.336 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.678 48.772 1529 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.99 % Allowed : 20.31 % Favored : 75.69 % 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: 0.91 (0.24), residues: 1308 helix: 1.94 (0.20), residues: 685 sheet: -0.29 (0.38), residues: 188 loop : -1.18 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE B 493 TYR 0.016 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 591) hydrogen bonds : angle 4.06787 ( 1710) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.83719 ( 6) covalent geometry : bond 0.00363 (10761) covalent geometry : angle 0.85727 (14571) ********************** 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 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8076 (mm) cc_final: 0.7858 (mt) REVERT: A 345 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7160 (tpp) REVERT: A 353 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7405 (mmm) REVERT: A 406 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: A 529 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 647 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6347 (t-170) REVERT: B 26 ARG cc_start: 0.6350 (ptt180) cc_final: 0.6136 (ptt180) REVERT: B 121 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5612 (mmt-90) REVERT: B 156 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: B 392 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: B 474 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 503 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: B 517 TRP cc_start: 0.7798 (m100) cc_final: 0.7004 (t60) REVERT: B 582 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.7164 (p) REVERT: C 26 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8522 (m) REVERT: C 88 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7610 (mtm-85) REVERT: C 94 ASP cc_start: 0.8284 (t0) cc_final: 0.8022 (t0) REVERT: C 99 ILE cc_start: 0.8906 (mt) cc_final: 0.8475 (mp) REVERT: C 103 GLN cc_start: 0.8371 (tp40) cc_final: 0.7549 (tp-100) REVERT: D 38 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7861 (ptm-80) REVERT: D 97 SER cc_start: 0.8284 (t) cc_final: 0.8035 (p) REVERT: D 125 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8073 (mt-10) outliers start: 46 outliers final: 29 residues processed: 173 average time/residue: 1.1757 time to fit residues: 219.7957 Evaluate side-chains 180 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 406 ARG 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 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 156 GLN 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 392 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 560 SER 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 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG 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 128 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.105955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.081192 restraints weight = 14160.165| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.05 r_work: 0.2788 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10764 Z= 0.163 Angle : 0.857 59.194 14577 Z= 0.482 Chirality : 0.041 0.336 1662 Planarity : 0.004 0.059 1828 Dihedral : 4.678 48.772 1529 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.82 % Allowed : 20.49 % Favored : 75.69 % 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: 0.91 (0.24), residues: 1308 helix: 1.94 (0.20), residues: 685 sheet: -0.29 (0.38), residues: 188 loop : -1.18 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE B 493 TYR 0.016 0.001 TYR A 114 ARG 0.009 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 591) hydrogen bonds : angle 4.06787 ( 1710) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.83719 ( 6) covalent geometry : bond 0.00363 (10761) covalent geometry : angle 0.85727 (14571) =============================================================================== Job complete usr+sys time: 8974.21 seconds wall clock time: 157 minutes 33.33 seconds (9453.33 seconds total)