Starting phenix.real_space_refine on Wed Apr 30 18:35:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.map" model { file = "/net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jji_61528/04_2025/9jji_61528.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.081 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 34 5.16 5 C 6407 2.51 5 N 1679 2.21 5 O 1901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10021 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 16, 'TRANS': 151} Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3673 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 447} Chain breaks: 2 Chain: "C" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 16, 'TRANS': 151} Chain: "D" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3752 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459} Time building chain proxies: 6.47, per 1000 atoms: 0.65 Number of scatterers: 10021 At special positions: 0 Unit cell: (116.62, 112.504, 116.62, 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 34 16.00 O 1901 8.00 N 1679 7.00 C 6407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 20 sheets defined 11.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.557A pdb=" N ARG A 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 100 through 107 removed outlier: 4.004A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.571A pdb=" N ARG B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.527A pdb=" N ASN B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.826A pdb=" N LEU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.937A pdb=" N ILE B 443 " --> pdb=" O PRO B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.013A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.632A pdb=" N ARG C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 70 " --> pdb=" O THR C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 70' Processing helix chain 'C' and resid 96 through 99 Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.995A pdb=" N VAL C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.777A pdb=" N ARG D 69 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.619A pdb=" N ASN D 100 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.703A pdb=" N LEU D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.921A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 5.834A pdb=" N TYR A 74 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR A 215 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 76 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.120A pdb=" N ILE A 89 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 194 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 91 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG A 132 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN A 197 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 130 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 81 removed outlier: 5.838A pdb=" N TYR B 74 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR B 215 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.673A pdb=" N LEU B 192 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B 92 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 190 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 132 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 197 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY B 130 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA7, first strand: chain 'B' and resid 485 through 488 removed outlier: 4.882A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 522 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 516 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 518 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 553 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 546 removed outlier: 7.674A pdb=" N ILE B 261 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL B 466 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 390 removed outlier: 4.463A pdb=" N TRP B 354 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.019A pdb=" N SER B 319 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N ARG B 299 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 420 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 416 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B 301 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR B 414 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 6.916A pdb=" N VAL C 213 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 77 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 211 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR C 79 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 209 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 94 removed outlier: 7.035A pdb=" N ILE C 89 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 194 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR C 91 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG C 132 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 197 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY C 130 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AB5, first strand: chain 'D' and resid 73 through 81 removed outlier: 5.904A pdb=" N TYR D 74 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N THR D 215 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN D 210 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 94 removed outlier: 6.717A pdb=" N LEU D 192 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR D 92 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 190 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG D 132 " --> pdb=" O TYR D 195 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN D 197 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY D 130 " --> pdb=" O ASN D 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AB8, first strand: chain 'D' and resid 485 through 488 removed outlier: 5.013A pdb=" N PHE D 534 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE D 512 " --> pdb=" O PRO D 558 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 514 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP D 552 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 545 through 546 removed outlier: 7.643A pdb=" N ILE D 261 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL D 466 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE D 534 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 523 " --> pdb=" O ASN D 568 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 295 through 297 removed outlier: 9.696A pdb=" N TRP D 354 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N ALA D 375 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N GLY D 356 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N MET D 373 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLY D 358 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR D 371 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE D 360 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.900A pdb=" N ILE D 360 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR D 371 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLY D 358 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N MET D 373 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N GLY D 356 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N ALA D 375 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N TRP D 354 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY D 353 " --> pdb=" O SER D 427 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 741 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: 3.26 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3264 1.34 - 1.46: 1854 1.46 - 1.57: 5135 1.57 - 1.69: 0 1.69 - 1.80: 66 Bond restraints: 10319 Sorted by residual: bond pdb=" C VAL D 384 " pdb=" N PRO D 385 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.30e-02 5.92e+03 1.39e+00 bond pdb=" C LEU B 163 " pdb=" N GLU B 164 " ideal model delta sigma weight residual 1.326 1.307 0.019 1.84e-02 2.95e+03 1.05e+00 bond pdb=" C SER D 288 " pdb=" N SER D 289 " ideal model delta sigma weight residual 1.331 1.302 0.029 2.83e-02 1.25e+03 1.03e+00 bond pdb=" N ASN D 183 " pdb=" CA ASN D 183 " ideal model delta sigma weight residual 1.463 1.453 0.011 1.08e-02 8.57e+03 9.64e-01 bond pdb=" CG LEU B 133 " pdb=" CD1 LEU B 133 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.55e-01 ... (remaining 10314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 13076 0.97 - 1.93: 840 1.93 - 2.90: 146 2.90 - 3.86: 89 3.86 - 4.83: 15 Bond angle restraints: 14166 Sorted by residual: angle pdb=" CA GLY D 131 " pdb=" C GLY D 131 " pdb=" N ARG D 132 " ideal model delta sigma weight residual 114.23 117.74 -3.51 8.80e-01 1.29e+00 1.59e+01 angle pdb=" CA GLY C 131 " pdb=" C GLY C 131 " pdb=" N ARG C 132 " ideal model delta sigma weight residual 115.34 117.97 -2.63 8.40e-01 1.42e+00 9.81e+00 angle pdb=" CA GLY D 131 " pdb=" C GLY D 131 " pdb=" O GLY D 131 " ideal model delta sigma weight residual 122.33 119.98 2.35 8.10e-01 1.52e+00 8.41e+00 angle pdb=" CA GLY A 131 " pdb=" C GLY A 131 " pdb=" N ARG A 132 " ideal model delta sigma weight residual 115.11 117.78 -2.67 9.50e-01 1.11e+00 7.93e+00 angle pdb=" CA VAL B 224 " pdb=" C VAL B 224 " pdb=" N MET B 225 " ideal model delta sigma weight residual 117.37 119.28 -1.91 7.40e-01 1.83e+00 6.64e+00 ... (remaining 14161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5591 17.87 - 35.74: 320 35.74 - 53.61: 52 53.61 - 71.48: 10 71.48 - 89.36: 11 Dihedral angle restraints: 5984 sinusoidal: 2226 harmonic: 3758 Sorted by residual: dihedral pdb=" CA TYR C 195 " pdb=" C TYR C 195 " pdb=" N ASN C 196 " pdb=" CA ASN C 196 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO C 154 " pdb=" C PRO C 154 " pdb=" N HIS C 155 " pdb=" CA HIS C 155 " ideal model delta harmonic sigma weight residual 180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLY B 383 " pdb=" C GLY B 383 " pdb=" N VAL B 384 " pdb=" CA VAL B 384 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 802 0.027 - 0.054: 430 0.054 - 0.081: 174 0.081 - 0.108: 125 0.108 - 0.135: 51 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CB ILE B 455 " pdb=" CA ILE B 455 " pdb=" CG1 ILE B 455 " pdb=" CG2 ILE B 455 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL D 444 " pdb=" N VAL D 444 " pdb=" C VAL D 444 " pdb=" CB VAL D 444 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL B 211 " pdb=" N VAL B 211 " pdb=" C VAL B 211 " pdb=" CB VAL B 211 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1579 not shown) Planarity restraints: 1869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 195 " -0.017 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR C 195 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 195 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 195 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 195 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 195 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 195 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 195 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 100 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 101 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 100 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO B 101 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.019 5.00e-02 4.00e+02 ... (remaining 1866 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1453 2.76 - 3.29: 9084 3.29 - 3.83: 15566 3.83 - 4.36: 17756 4.36 - 4.90: 33162 Nonbonded interactions: 77021 Sorted by model distance: nonbonded pdb=" O PRO A 97 " pdb=" OG1 THR A 103 " model vdw 2.221 3.040 nonbonded pdb=" O TYR A 110 " pdb=" NH1 ARG A 227 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLU D 66 " pdb=" NE1 TRP D 68 " model vdw 2.259 3.120 nonbonded pdb=" O THR D 245 " pdb=" OG1 THR D 249 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 159 " pdb=" N ALA A 160 " model vdw 2.265 3.120 ... (remaining 77016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 66 through 230 or resid 239 through 305 or resid 310 throu \ gh 569)) } 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.840 Find NCS groups from input model: 0.360 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.005 0.032 10319 Z= 0.197 Angle : 0.601 4.830 14166 Z= 0.325 Chirality : 0.047 0.135 1582 Planarity : 0.004 0.038 1869 Dihedral : 12.411 89.356 3598 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.45 (0.22), residues: 1320 helix: -0.62 (0.88), residues: 46 sheet: 0.32 (0.25), residues: 413 loop : -0.58 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 278 HIS 0.004 0.001 HIS D 179 PHE 0.019 0.002 PHE B 357 TYR 0.029 0.002 TYR C 195 ARG 0.005 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.25347 ( 292) hydrogen bonds : angle 9.95872 ( 741) covalent geometry : bond 0.00458 (10319) covalent geometry : angle 0.60130 (14166) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.152 Fit side-chains REVERT: A 93 VAL cc_start: 0.8219 (p) cc_final: 0.7776 (m) REVERT: A 128 VAL cc_start: 0.8462 (m) cc_final: 0.8201 (t) REVERT: A 206 THR cc_start: 0.8789 (m) cc_final: 0.8135 (p) REVERT: B 74 TYR cc_start: 0.8735 (t80) cc_final: 0.8204 (t80) REVERT: B 109 MET cc_start: 0.7960 (ptp) cc_final: 0.7720 (ptm) REVERT: B 143 GLU cc_start: 0.7686 (pp20) cc_final: 0.7388 (pp20) REVERT: B 149 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 161 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.8208 (ptt180) REVERT: B 168 ILE cc_start: 0.8379 (tp) cc_final: 0.8128 (tt) REVERT: B 170 MET cc_start: 0.7970 (ttm) cc_final: 0.7726 (ttp) REVERT: B 219 GLU cc_start: 0.6896 (mp0) cc_final: 0.6644 (mp0) REVERT: B 295 ILE cc_start: 0.8091 (mt) cc_final: 0.7755 (mt) REVERT: B 298 ASP cc_start: 0.7338 (p0) cc_final: 0.6884 (p0) REVERT: B 328 ILE cc_start: 0.9289 (tt) cc_final: 0.8881 (tt) REVERT: B 365 ASN cc_start: 0.8064 (p0) cc_final: 0.7582 (p0) REVERT: B 398 GLN cc_start: 0.8052 (mt0) cc_final: 0.7640 (mt0) REVERT: B 413 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7978 (mm-40) REVERT: B 455 ILE cc_start: 0.8249 (tp) cc_final: 0.7963 (pt) REVERT: B 530 VAL cc_start: 0.8835 (t) cc_final: 0.8629 (p) REVERT: B 535 TYR cc_start: 0.8601 (m-80) cc_final: 0.8131 (m-10) REVERT: B 546 ASP cc_start: 0.7500 (t70) cc_final: 0.7097 (t0) REVERT: B 548 SER cc_start: 0.8357 (m) cc_final: 0.7946 (p) REVERT: B 552 ASP cc_start: 0.7437 (p0) cc_final: 0.7072 (p0) REVERT: B 566 VAL cc_start: 0.8871 (t) cc_final: 0.8617 (m) REVERT: C 129 PHE cc_start: 0.8461 (m-80) cc_final: 0.7765 (m-80) REVERT: C 225 MET cc_start: 0.6588 (mtt) cc_final: 0.6378 (mtm) REVERT: D 151 ARG cc_start: 0.8311 (ptt180) cc_final: 0.6905 (ptm160) REVERT: D 152 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7581 (mt0) REVERT: D 210 GLN cc_start: 0.8068 (mm110) cc_final: 0.7820 (mm110) REVERT: D 260 GLU cc_start: 0.7159 (pt0) cc_final: 0.6925 (pt0) REVERT: D 271 PHE cc_start: 0.8727 (p90) cc_final: 0.8457 (p90) REVERT: D 344 PHE cc_start: 0.8440 (p90) cc_final: 0.8230 (p90) REVERT: D 362 ASN cc_start: 0.7929 (t0) cc_final: 0.7330 (t0) REVERT: D 364 SER cc_start: 0.8679 (m) cc_final: 0.8342 (p) REVERT: D 373 MET cc_start: 0.7772 (mmm) cc_final: 0.7340 (mmm) REVERT: D 377 GLU cc_start: 0.7951 (tt0) cc_final: 0.7344 (tt0) REVERT: D 389 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7169 (mm-40) REVERT: D 412 ASN cc_start: 0.7895 (m110) cc_final: 0.7528 (m110) REVERT: D 428 THR cc_start: 0.8215 (p) cc_final: 0.7906 (p) REVERT: D 435 THR cc_start: 0.7900 (p) cc_final: 0.7534 (t) REVERT: D 466 VAL cc_start: 0.8490 (t) cc_final: 0.8223 (p) REVERT: D 511 GLN cc_start: 0.8449 (mt0) cc_final: 0.7404 (mt0) REVERT: D 514 VAL cc_start: 0.8719 (t) cc_final: 0.8210 (p) REVERT: D 523 PHE cc_start: 0.8376 (p90) cc_final: 0.8005 (p90) REVERT: D 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7437 (m-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2063 time to fit residues: 83.7817 Evaluate side-chains 254 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 0.0010 chunk 118 optimal weight: 9.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 210 GLN B 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085087 restraints weight = 16838.118| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.37 r_work: 0.2840 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10319 Z= 0.160 Angle : 0.581 7.359 14166 Z= 0.296 Chirality : 0.048 0.176 1582 Planarity : 0.005 0.042 1869 Dihedral : 4.187 18.283 1422 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.47 % Allowed : 9.22 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1320 helix: -1.02 (0.78), residues: 50 sheet: 0.51 (0.25), residues: 404 loop : -0.72 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 316 HIS 0.006 0.002 HIS C 179 PHE 0.015 0.002 PHE B 78 TYR 0.014 0.002 TYR D 91 ARG 0.004 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 292) hydrogen bonds : angle 7.14483 ( 741) covalent geometry : bond 0.00373 (10319) covalent geometry : angle 0.58059 (14166) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 1.150 Fit side-chains REVERT: A 113 TRP cc_start: 0.8967 (p-90) cc_final: 0.8278 (p-90) REVERT: A 128 VAL cc_start: 0.8491 (m) cc_final: 0.8215 (t) REVERT: A 206 THR cc_start: 0.8905 (m) cc_final: 0.8326 (p) REVERT: A 225 MET cc_start: 0.7540 (mtt) cc_final: 0.7338 (mtt) REVERT: B 74 TYR cc_start: 0.8804 (t80) cc_final: 0.8225 (t80) REVERT: B 143 GLU cc_start: 0.8262 (pp20) cc_final: 0.7925 (pp20) REVERT: B 161 ARG cc_start: 0.8625 (ptt-90) cc_final: 0.8379 (ptt180) REVERT: B 227 ARG cc_start: 0.8550 (ptt180) cc_final: 0.8334 (ptt-90) REVERT: B 262 VAL cc_start: 0.9031 (m) cc_final: 0.8642 (t) REVERT: B 295 ILE cc_start: 0.8210 (mt) cc_final: 0.7885 (mt) REVERT: B 298 ASP cc_start: 0.7438 (p0) cc_final: 0.7070 (p0) REVERT: B 369 TYR cc_start: 0.8031 (m-10) cc_final: 0.7772 (m-10) REVERT: B 398 GLN cc_start: 0.8364 (mt0) cc_final: 0.8060 (mt0) REVERT: B 413 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8372 (mm-40) REVERT: B 444 VAL cc_start: 0.8713 (t) cc_final: 0.8337 (m) REVERT: B 455 ILE cc_start: 0.8447 (tp) cc_final: 0.8140 (pt) REVERT: B 468 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7997 (mtt90) REVERT: B 530 VAL cc_start: 0.8831 (t) cc_final: 0.8611 (p) REVERT: B 546 ASP cc_start: 0.7922 (t70) cc_final: 0.7606 (t0) REVERT: B 548 SER cc_start: 0.8652 (m) cc_final: 0.8327 (p) REVERT: B 566 VAL cc_start: 0.8838 (t) cc_final: 0.8613 (m) REVERT: C 99 ASN cc_start: 0.8091 (m-40) cc_final: 0.7787 (m110) REVERT: D 151 ARG cc_start: 0.8677 (ptt180) cc_final: 0.6922 (ttt180) REVERT: D 152 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7525 (mm-40) REVERT: D 210 GLN cc_start: 0.8387 (mm110) cc_final: 0.8087 (mm110) REVERT: D 213 VAL cc_start: 0.7907 (t) cc_final: 0.7684 (m) REVERT: D 271 PHE cc_start: 0.8876 (p90) cc_final: 0.8495 (p90) REVERT: D 344 PHE cc_start: 0.8376 (p90) cc_final: 0.8125 (p90) REVERT: D 362 ASN cc_start: 0.8238 (t0) cc_final: 0.7742 (t0) REVERT: D 364 SER cc_start: 0.8840 (m) cc_final: 0.8495 (p) REVERT: D 373 MET cc_start: 0.8199 (mmm) cc_final: 0.7741 (mmm) REVERT: D 377 GLU cc_start: 0.8467 (tt0) cc_final: 0.7863 (tt0) REVERT: D 387 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.6971 (p0) REVERT: D 428 THR cc_start: 0.8557 (p) cc_final: 0.8240 (t) REVERT: D 466 VAL cc_start: 0.8675 (t) cc_final: 0.8340 (p) REVERT: D 511 GLN cc_start: 0.8734 (mt0) cc_final: 0.8460 (mt0) REVERT: D 514 VAL cc_start: 0.8642 (t) cc_final: 0.8406 (m) REVERT: D 523 PHE cc_start: 0.8252 (p90) cc_final: 0.7938 (p90) REVERT: D 549 ASP cc_start: 0.8074 (m-30) cc_final: 0.7850 (m-30) REVERT: D 566 VAL cc_start: 0.8485 (t) cc_final: 0.8221 (t) outliers start: 16 outliers final: 15 residues processed: 264 average time/residue: 0.2100 time to fit residues: 78.9834 Evaluate side-chains 256 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS C 176 ASN D 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.082963 restraints weight = 17378.313| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.54 r_work: 0.2808 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10319 Z= 0.134 Angle : 0.540 6.908 14166 Z= 0.274 Chirality : 0.047 0.171 1582 Planarity : 0.005 0.040 1869 Dihedral : 4.024 17.175 1422 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.49 % Allowed : 11.52 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.49 (0.22), residues: 1320 helix: -0.94 (0.79), residues: 50 sheet: 0.59 (0.25), residues: 396 loop : -0.75 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 68 HIS 0.004 0.001 HIS C 179 PHE 0.013 0.001 PHE D 223 TYR 0.012 0.001 TYR D 91 ARG 0.003 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 292) hydrogen bonds : angle 6.60534 ( 741) covalent geometry : bond 0.00314 (10319) covalent geometry : angle 0.54014 (14166) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8943 (p-90) cc_final: 0.8244 (p-90) REVERT: A 128 VAL cc_start: 0.8415 (m) cc_final: 0.8171 (t) REVERT: A 206 THR cc_start: 0.8880 (m) cc_final: 0.8292 (p) REVERT: A 225 MET cc_start: 0.7551 (mtt) cc_final: 0.7333 (mtt) REVERT: B 74 TYR cc_start: 0.8835 (t80) cc_final: 0.8243 (t80) REVERT: B 143 GLU cc_start: 0.8261 (pp20) cc_final: 0.7916 (pp20) REVERT: B 262 VAL cc_start: 0.8968 (m) cc_final: 0.8732 (t) REVERT: B 295 ILE cc_start: 0.8207 (mt) cc_final: 0.7890 (mt) REVERT: B 298 ASP cc_start: 0.7577 (p0) cc_final: 0.7225 (p0) REVERT: B 369 TYR cc_start: 0.8117 (m-10) cc_final: 0.7787 (m-10) REVERT: B 372 THR cc_start: 0.8591 (p) cc_final: 0.8054 (t) REVERT: B 387 ASN cc_start: 0.7155 (t0) cc_final: 0.6596 (t0) REVERT: B 398 GLN cc_start: 0.8374 (mt0) cc_final: 0.8086 (mt0) REVERT: B 413 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8366 (mm-40) REVERT: B 444 VAL cc_start: 0.8788 (t) cc_final: 0.8433 (m) REVERT: B 530 VAL cc_start: 0.8890 (t) cc_final: 0.8665 (p) REVERT: B 546 ASP cc_start: 0.7903 (t70) cc_final: 0.7629 (t0) REVERT: B 548 SER cc_start: 0.8659 (m) cc_final: 0.8276 (p) REVERT: B 559 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7801 (tpp80) REVERT: B 566 VAL cc_start: 0.8847 (t) cc_final: 0.8623 (m) REVERT: C 99 ASN cc_start: 0.8102 (m-40) cc_final: 0.7729 (m110) REVERT: C 129 PHE cc_start: 0.8618 (m-80) cc_final: 0.7898 (m-80) REVERT: C 176 ASN cc_start: 0.8513 (m-40) cc_final: 0.8281 (m-40) REVERT: C 177 MET cc_start: 0.7807 (mmt) cc_final: 0.7177 (mmt) REVERT: D 151 ARG cc_start: 0.8664 (ptt180) cc_final: 0.7157 (ptm160) REVERT: D 177 MET cc_start: 0.7940 (mmm) cc_final: 0.7147 (mmt) REVERT: D 210 GLN cc_start: 0.8371 (mm110) cc_final: 0.8040 (mm110) REVERT: D 213 VAL cc_start: 0.7919 (t) cc_final: 0.7625 (m) REVERT: D 271 PHE cc_start: 0.8929 (p90) cc_final: 0.8632 (p90) REVERT: D 344 PHE cc_start: 0.8390 (p90) cc_final: 0.8032 (p90) REVERT: D 362 ASN cc_start: 0.8325 (t0) cc_final: 0.7759 (t0) REVERT: D 364 SER cc_start: 0.8875 (m) cc_final: 0.8546 (p) REVERT: D 373 MET cc_start: 0.8265 (mmm) cc_final: 0.7748 (mmm) REVERT: D 377 GLU cc_start: 0.8524 (tt0) cc_final: 0.7872 (tt0) REVERT: D 380 PHE cc_start: 0.8123 (m-80) cc_final: 0.7786 (m-80) REVERT: D 387 ASN cc_start: 0.8048 (t0) cc_final: 0.7161 (p0) REVERT: D 428 THR cc_start: 0.8587 (p) cc_final: 0.8328 (t) REVERT: D 466 VAL cc_start: 0.8622 (t) cc_final: 0.8302 (p) REVERT: D 511 GLN cc_start: 0.8755 (mt0) cc_final: 0.7812 (mt0) REVERT: D 514 VAL cc_start: 0.8681 (t) cc_final: 0.8392 (m) REVERT: D 523 PHE cc_start: 0.8146 (p90) cc_final: 0.7798 (p90) REVERT: D 566 VAL cc_start: 0.8525 (t) cc_final: 0.7890 (m) outliers start: 27 outliers final: 19 residues processed: 266 average time/residue: 0.2099 time to fit residues: 79.0298 Evaluate side-chains 266 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 0.0060 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS D 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.082996 restraints weight = 17185.163| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.48 r_work: 0.2865 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10319 Z= 0.141 Angle : 0.542 8.093 14166 Z= 0.274 Chirality : 0.047 0.145 1582 Planarity : 0.005 0.038 1869 Dihedral : 4.012 17.455 1422 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.23 % Allowed : 12.35 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1320 helix: -0.86 (0.79), residues: 50 sheet: 0.48 (0.26), residues: 395 loop : -0.71 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 68 HIS 0.004 0.001 HIS C 179 PHE 0.013 0.001 PHE B 78 TYR 0.013 0.001 TYR D 91 ARG 0.003 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 292) hydrogen bonds : angle 6.45128 ( 741) covalent geometry : bond 0.00332 (10319) covalent geometry : angle 0.54217 (14166) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8943 (p-90) cc_final: 0.8272 (p-90) REVERT: A 128 VAL cc_start: 0.8460 (m) cc_final: 0.8206 (t) REVERT: A 195 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 206 THR cc_start: 0.8897 (m) cc_final: 0.8427 (t) REVERT: B 74 TYR cc_start: 0.8839 (t80) cc_final: 0.8273 (t80) REVERT: B 75 ASN cc_start: 0.8466 (t0) cc_final: 0.8164 (t0) REVERT: B 143 GLU cc_start: 0.8248 (pp20) cc_final: 0.7922 (pp20) REVERT: B 169 THR cc_start: 0.8595 (m) cc_final: 0.8387 (p) REVERT: B 177 MET cc_start: 0.8670 (mmm) cc_final: 0.8380 (mmp) REVERT: B 295 ILE cc_start: 0.8286 (mt) cc_final: 0.7925 (mt) REVERT: B 298 ASP cc_start: 0.7622 (p0) cc_final: 0.7214 (p0) REVERT: B 349 ILE cc_start: 0.8435 (mp) cc_final: 0.8211 (mm) REVERT: B 372 THR cc_start: 0.8571 (p) cc_final: 0.8109 (t) REVERT: B 387 ASN cc_start: 0.7210 (t0) cc_final: 0.6730 (t0) REVERT: B 398 GLN cc_start: 0.8290 (mt0) cc_final: 0.8005 (mt0) REVERT: B 409 ASN cc_start: 0.8420 (m-40) cc_final: 0.8139 (m-40) REVERT: B 413 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8366 (mm-40) REVERT: B 444 VAL cc_start: 0.8828 (t) cc_final: 0.8474 (m) REVERT: B 530 VAL cc_start: 0.8950 (t) cc_final: 0.8725 (p) REVERT: B 546 ASP cc_start: 0.7897 (t70) cc_final: 0.7630 (t0) REVERT: B 548 SER cc_start: 0.8583 (m) cc_final: 0.8205 (p) REVERT: B 559 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7808 (tpp80) REVERT: B 566 VAL cc_start: 0.8836 (t) cc_final: 0.8612 (m) REVERT: C 99 ASN cc_start: 0.8096 (m-40) cc_final: 0.7871 (m-40) REVERT: D 151 ARG cc_start: 0.8691 (ptt180) cc_final: 0.6955 (ttt180) REVERT: D 213 VAL cc_start: 0.7960 (t) cc_final: 0.7659 (p) REVERT: D 271 PHE cc_start: 0.8895 (p90) cc_final: 0.8543 (p90) REVERT: D 316 TRP cc_start: 0.8499 (t60) cc_final: 0.8172 (t60) REVERT: D 344 PHE cc_start: 0.8394 (p90) cc_final: 0.7941 (p90) REVERT: D 362 ASN cc_start: 0.8375 (t0) cc_final: 0.7825 (t0) REVERT: D 364 SER cc_start: 0.8868 (m) cc_final: 0.8544 (p) REVERT: D 373 MET cc_start: 0.8230 (mmm) cc_final: 0.7785 (mmm) REVERT: D 377 GLU cc_start: 0.8463 (tt0) cc_final: 0.7770 (tt0) REVERT: D 380 PHE cc_start: 0.8083 (m-80) cc_final: 0.7789 (m-80) REVERT: D 387 ASN cc_start: 0.8169 (t0) cc_final: 0.7688 (p0) REVERT: D 428 THR cc_start: 0.8655 (p) cc_final: 0.8387 (t) REVERT: D 466 VAL cc_start: 0.8609 (t) cc_final: 0.8288 (p) REVERT: D 511 GLN cc_start: 0.8771 (mt0) cc_final: 0.7850 (mt0) REVERT: D 514 VAL cc_start: 0.8714 (t) cc_final: 0.8436 (m) REVERT: D 523 PHE cc_start: 0.8132 (p90) cc_final: 0.7828 (p90) REVERT: D 525 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 566 VAL cc_start: 0.8542 (t) cc_final: 0.8120 (m) outliers start: 35 outliers final: 29 residues processed: 277 average time/residue: 0.2179 time to fit residues: 86.8909 Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.088119 restraints weight = 16722.582| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.35 r_work: 0.2863 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10319 Z= 0.105 Angle : 0.511 8.589 14166 Z= 0.256 Chirality : 0.046 0.146 1582 Planarity : 0.005 0.037 1869 Dihedral : 3.844 16.708 1422 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.41 % Allowed : 13.36 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.42 (0.22), residues: 1320 helix: -0.56 (0.81), residues: 50 sheet: 0.54 (0.26), residues: 402 loop : -0.66 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 68 HIS 0.004 0.001 HIS D 277 PHE 0.011 0.001 PHE A 221 TYR 0.011 0.001 TYR D 91 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 292) hydrogen bonds : angle 6.22333 ( 741) covalent geometry : bond 0.00247 (10319) covalent geometry : angle 0.51069 (14166) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8959 (p-90) cc_final: 0.8311 (p-90) REVERT: A 206 THR cc_start: 0.8856 (m) cc_final: 0.8416 (t) REVERT: B 74 TYR cc_start: 0.8830 (t80) cc_final: 0.8241 (t80) REVERT: B 75 ASN cc_start: 0.8403 (t0) cc_final: 0.8127 (t0) REVERT: B 151 ARG cc_start: 0.5892 (ptm160) cc_final: 0.5521 (ptm160) REVERT: B 177 MET cc_start: 0.8617 (mmm) cc_final: 0.8377 (mmp) REVERT: B 295 ILE cc_start: 0.8291 (mt) cc_final: 0.7922 (mt) REVERT: B 298 ASP cc_start: 0.7639 (p0) cc_final: 0.7239 (p0) REVERT: B 349 ILE cc_start: 0.8434 (mp) cc_final: 0.8209 (mm) REVERT: B 372 THR cc_start: 0.8543 (p) cc_final: 0.8094 (t) REVERT: B 373 MET cc_start: 0.8814 (mmp) cc_final: 0.8338 (mmp) REVERT: B 398 GLN cc_start: 0.8257 (mt0) cc_final: 0.7998 (mt0) REVERT: B 409 ASN cc_start: 0.8410 (m-40) cc_final: 0.8092 (m-40) REVERT: B 413 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8322 (mm-40) REVERT: B 427 SER cc_start: 0.8336 (p) cc_final: 0.8132 (p) REVERT: B 444 VAL cc_start: 0.8820 (t) cc_final: 0.8475 (m) REVERT: B 481 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6659 (t160) REVERT: B 518 ASN cc_start: 0.8094 (m-40) cc_final: 0.7700 (t0) REVERT: B 530 VAL cc_start: 0.8870 (t) cc_final: 0.8659 (p) REVERT: B 546 ASP cc_start: 0.7839 (t70) cc_final: 0.7611 (t0) REVERT: B 548 SER cc_start: 0.8529 (m) cc_final: 0.8195 (p) REVERT: B 566 VAL cc_start: 0.8835 (t) cc_final: 0.8616 (m) REVERT: C 99 ASN cc_start: 0.8076 (m-40) cc_final: 0.7859 (m-40) REVERT: C 129 PHE cc_start: 0.8632 (m-80) cc_final: 0.7930 (m-80) REVERT: D 151 ARG cc_start: 0.8684 (ptt180) cc_final: 0.6959 (ttt180) REVERT: D 271 PHE cc_start: 0.8890 (p90) cc_final: 0.8562 (p90) REVERT: D 344 PHE cc_start: 0.8402 (p90) cc_final: 0.7863 (p90) REVERT: D 362 ASN cc_start: 0.8317 (t0) cc_final: 0.7831 (t0) REVERT: D 364 SER cc_start: 0.8853 (m) cc_final: 0.8535 (p) REVERT: D 373 MET cc_start: 0.8248 (mmm) cc_final: 0.7669 (mmm) REVERT: D 377 GLU cc_start: 0.8443 (tt0) cc_final: 0.7772 (tt0) REVERT: D 380 PHE cc_start: 0.7982 (m-80) cc_final: 0.7736 (m-80) REVERT: D 387 ASN cc_start: 0.8163 (t0) cc_final: 0.7688 (p0) REVERT: D 428 THR cc_start: 0.8679 (p) cc_final: 0.8416 (t) REVERT: D 466 VAL cc_start: 0.8542 (t) cc_final: 0.8219 (p) REVERT: D 511 GLN cc_start: 0.8758 (mt0) cc_final: 0.7928 (mt0) REVERT: D 514 VAL cc_start: 0.8705 (t) cc_final: 0.8438 (m) REVERT: D 523 PHE cc_start: 0.8139 (p90) cc_final: 0.7840 (p90) REVERT: D 566 VAL cc_start: 0.8489 (t) cc_final: 0.8146 (m) outliers start: 37 outliers final: 29 residues processed: 278 average time/residue: 0.2078 time to fit residues: 82.8378 Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 126 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 2.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN D 412 ASN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.083401 restraints weight = 17345.744| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.54 r_work: 0.2834 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10319 Z= 0.145 Angle : 0.541 9.239 14166 Z= 0.271 Chirality : 0.047 0.177 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.948 17.310 1422 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.59 % Allowed : 14.47 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.56 (0.22), residues: 1320 helix: -0.54 (0.80), residues: 50 sheet: 0.30 (0.26), residues: 390 loop : -0.68 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 68 HIS 0.005 0.001 HIS C 179 PHE 0.012 0.001 PHE B 78 TYR 0.015 0.001 TYR D 91 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 292) hydrogen bonds : angle 6.21642 ( 741) covalent geometry : bond 0.00340 (10319) covalent geometry : angle 0.54098 (14166) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8965 (p-90) cc_final: 0.8241 (p-90) REVERT: A 206 THR cc_start: 0.8874 (m) cc_final: 0.8437 (t) REVERT: B 74 TYR cc_start: 0.8836 (t80) cc_final: 0.8272 (t80) REVERT: B 75 ASN cc_start: 0.8449 (t0) cc_final: 0.8153 (t0) REVERT: B 143 GLU cc_start: 0.8280 (pp20) cc_final: 0.7938 (pp20) REVERT: B 149 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 151 ARG cc_start: 0.5809 (ptm160) cc_final: 0.5437 (ptm160) REVERT: B 177 MET cc_start: 0.8690 (mmm) cc_final: 0.8397 (mmp) REVERT: B 219 GLU cc_start: 0.7757 (mp0) cc_final: 0.7363 (mp0) REVERT: B 257 TRP cc_start: 0.8960 (m100) cc_final: 0.8736 (m100) REVERT: B 295 ILE cc_start: 0.8324 (mt) cc_final: 0.7938 (mt) REVERT: B 298 ASP cc_start: 0.7726 (p0) cc_final: 0.7333 (p0) REVERT: B 349 ILE cc_start: 0.8431 (mp) cc_final: 0.8210 (mm) REVERT: B 372 THR cc_start: 0.8541 (p) cc_final: 0.8098 (t) REVERT: B 373 MET cc_start: 0.8786 (mmp) cc_final: 0.8271 (mmp) REVERT: B 377 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 398 GLN cc_start: 0.8338 (mt0) cc_final: 0.8053 (mt0) REVERT: B 413 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8321 (mm-40) REVERT: B 444 VAL cc_start: 0.8870 (t) cc_final: 0.8543 (m) REVERT: B 481 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6680 (t160) REVERT: B 530 VAL cc_start: 0.8873 (t) cc_final: 0.8663 (p) REVERT: B 546 ASP cc_start: 0.7910 (t70) cc_final: 0.7654 (t0) REVERT: B 548 SER cc_start: 0.8519 (m) cc_final: 0.8208 (p) REVERT: B 566 VAL cc_start: 0.8852 (t) cc_final: 0.8432 (p) REVERT: C 72 PHE cc_start: 0.8396 (m-80) cc_final: 0.8121 (m-80) REVERT: C 99 ASN cc_start: 0.8118 (m-40) cc_final: 0.7900 (m110) REVERT: D 82 VAL cc_start: 0.8957 (p) cc_final: 0.8582 (t) REVERT: D 151 ARG cc_start: 0.8660 (ptt180) cc_final: 0.6905 (ttt180) REVERT: D 177 MET cc_start: 0.7971 (mmm) cc_final: 0.7713 (mmm) REVERT: D 271 PHE cc_start: 0.8902 (p90) cc_final: 0.8540 (p90) REVERT: D 304 PHE cc_start: 0.8411 (p90) cc_final: 0.8134 (p90) REVERT: D 344 PHE cc_start: 0.8444 (p90) cc_final: 0.7905 (p90) REVERT: D 362 ASN cc_start: 0.8328 (t0) cc_final: 0.7816 (t0) REVERT: D 364 SER cc_start: 0.8856 (m) cc_final: 0.8508 (p) REVERT: D 372 THR cc_start: 0.8570 (p) cc_final: 0.8058 (t) REVERT: D 373 MET cc_start: 0.8268 (mmm) cc_final: 0.7910 (mmm) REVERT: D 377 GLU cc_start: 0.8477 (tt0) cc_final: 0.7773 (tt0) REVERT: D 380 PHE cc_start: 0.8018 (m-80) cc_final: 0.7716 (m-80) REVERT: D 387 ASN cc_start: 0.8194 (t0) cc_final: 0.7578 (p0) REVERT: D 419 PHE cc_start: 0.8625 (t80) cc_final: 0.8423 (t80) REVERT: D 420 VAL cc_start: 0.8809 (t) cc_final: 0.8518 (m) REVERT: D 428 THR cc_start: 0.8673 (p) cc_final: 0.8395 (t) REVERT: D 466 VAL cc_start: 0.8613 (t) cc_final: 0.8290 (p) REVERT: D 511 GLN cc_start: 0.8764 (mt0) cc_final: 0.7829 (mt0) REVERT: D 566 VAL cc_start: 0.8448 (t) cc_final: 0.8118 (m) outliers start: 39 outliers final: 32 residues processed: 289 average time/residue: 0.2101 time to fit residues: 87.2687 Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 125 optimal weight: 0.0070 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083837 restraints weight = 17430.811| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.48 r_work: 0.2858 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10319 Z= 0.214 Angle : 0.583 10.134 14166 Z= 0.297 Chirality : 0.048 0.146 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.235 18.573 1422 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.78 % Allowed : 15.76 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1320 helix: -0.68 (0.78), residues: 50 sheet: 0.16 (0.26), residues: 404 loop : -0.75 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 68 HIS 0.005 0.002 HIS C 179 PHE 0.023 0.002 PHE D 523 TYR 0.018 0.002 TYR D 91 ARG 0.003 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 292) hydrogen bonds : angle 6.37447 ( 741) covalent geometry : bond 0.00501 (10319) covalent geometry : angle 0.58294 (14166) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.400 Fit side-chains REVERT: A 123 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8457 (m) REVERT: A 206 THR cc_start: 0.8944 (m) cc_final: 0.8528 (t) REVERT: B 74 TYR cc_start: 0.8867 (t80) cc_final: 0.8399 (t80) REVERT: B 75 ASN cc_start: 0.8517 (t0) cc_final: 0.8178 (t0) REVERT: B 143 GLU cc_start: 0.8269 (pp20) cc_final: 0.7911 (pp20) REVERT: B 149 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 177 MET cc_start: 0.8703 (mmm) cc_final: 0.8427 (mmp) REVERT: B 219 GLU cc_start: 0.7779 (mp0) cc_final: 0.7387 (mp0) REVERT: B 249 THR cc_start: 0.8127 (t) cc_final: 0.7924 (t) REVERT: B 257 TRP cc_start: 0.8939 (m100) cc_final: 0.8729 (m100) REVERT: B 295 ILE cc_start: 0.8353 (mt) cc_final: 0.8004 (mt) REVERT: B 298 ASP cc_start: 0.7804 (p0) cc_final: 0.7441 (p0) REVERT: B 349 ILE cc_start: 0.8451 (mp) cc_final: 0.8242 (mm) REVERT: B 369 TYR cc_start: 0.8109 (m-10) cc_final: 0.7787 (m-10) REVERT: B 372 THR cc_start: 0.8558 (p) cc_final: 0.8105 (t) REVERT: B 377 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 398 GLN cc_start: 0.8331 (mt0) cc_final: 0.8022 (mt0) REVERT: B 413 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 444 VAL cc_start: 0.8885 (t) cc_final: 0.8578 (m) REVERT: B 481 ASN cc_start: 0.7071 (OUTLIER) cc_final: 0.6671 (t0) REVERT: B 530 VAL cc_start: 0.8870 (t) cc_final: 0.8654 (p) REVERT: B 546 ASP cc_start: 0.7970 (t70) cc_final: 0.7731 (t0) REVERT: B 548 SER cc_start: 0.8563 (m) cc_final: 0.8170 (p) REVERT: B 566 VAL cc_start: 0.8926 (t) cc_final: 0.8577 (p) REVERT: D 82 VAL cc_start: 0.8982 (p) cc_final: 0.8632 (t) REVERT: D 149 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 151 ARG cc_start: 0.8686 (ptt180) cc_final: 0.6907 (ttt180) REVERT: D 271 PHE cc_start: 0.8889 (p90) cc_final: 0.8549 (p90) REVERT: D 275 ASN cc_start: 0.8463 (t0) cc_final: 0.8219 (t0) REVERT: D 304 PHE cc_start: 0.8490 (p90) cc_final: 0.8156 (p90) REVERT: D 344 PHE cc_start: 0.8421 (p90) cc_final: 0.7789 (p90) REVERT: D 362 ASN cc_start: 0.8365 (t0) cc_final: 0.7825 (t0) REVERT: D 364 SER cc_start: 0.8858 (m) cc_final: 0.8520 (p) REVERT: D 372 THR cc_start: 0.8654 (p) cc_final: 0.8196 (t) REVERT: D 373 MET cc_start: 0.8293 (mmm) cc_final: 0.7681 (mmm) REVERT: D 377 GLU cc_start: 0.8449 (tt0) cc_final: 0.7752 (tt0) REVERT: D 387 ASN cc_start: 0.8212 (t0) cc_final: 0.7491 (p0) REVERT: D 420 VAL cc_start: 0.8893 (t) cc_final: 0.8578 (m) REVERT: D 428 THR cc_start: 0.8687 (p) cc_final: 0.8428 (t) REVERT: D 466 VAL cc_start: 0.8650 (t) cc_final: 0.8374 (p) REVERT: D 474 ASN cc_start: 0.8290 (t0) cc_final: 0.7981 (t0) REVERT: D 511 GLN cc_start: 0.8770 (mt0) cc_final: 0.7866 (mt0) REVERT: D 514 VAL cc_start: 0.8749 (t) cc_final: 0.8459 (m) REVERT: D 566 VAL cc_start: 0.8532 (t) cc_final: 0.8076 (m) outliers start: 41 outliers final: 32 residues processed: 287 average time/residue: 0.2200 time to fit residues: 90.7061 Evaluate side-chains 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 0.0370 chunk 58 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 99 ASN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084481 restraints weight = 17240.566| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.53 r_work: 0.2846 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10319 Z= 0.108 Angle : 0.537 11.434 14166 Z= 0.269 Chirality : 0.047 0.143 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.991 18.369 1422 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.04 % Allowed : 17.24 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1320 helix: -0.39 (0.81), residues: 50 sheet: 0.18 (0.26), residues: 390 loop : -0.72 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 68 HIS 0.003 0.001 HIS D 277 PHE 0.022 0.001 PHE D 523 TYR 0.011 0.001 TYR D 91 ARG 0.003 0.000 ARG B 554 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 292) hydrogen bonds : angle 6.18315 ( 741) covalent geometry : bond 0.00255 (10319) covalent geometry : angle 0.53713 (14166) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 79 THR cc_start: 0.8609 (m) cc_final: 0.8406 (p) REVERT: A 113 TRP cc_start: 0.8937 (p-90) cc_final: 0.8182 (p-90) REVERT: A 123 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8486 (m) REVERT: A 206 THR cc_start: 0.8921 (m) cc_final: 0.8368 (p) REVERT: A 227 ARG cc_start: 0.8654 (ptt-90) cc_final: 0.8420 (ptt-90) REVERT: B 74 TYR cc_start: 0.8810 (t80) cc_final: 0.8298 (t80) REVERT: B 75 ASN cc_start: 0.8430 (t0) cc_final: 0.8151 (t0) REVERT: B 143 GLU cc_start: 0.8266 (pp20) cc_final: 0.7905 (pp20) REVERT: B 149 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7032 (mm-30) REVERT: B 151 ARG cc_start: 0.5797 (ptm160) cc_final: 0.5465 (ptm160) REVERT: B 168 ILE cc_start: 0.8429 (tp) cc_final: 0.8176 (tt) REVERT: B 177 MET cc_start: 0.8705 (mmm) cc_final: 0.8440 (mmp) REVERT: B 219 GLU cc_start: 0.7746 (mp0) cc_final: 0.7344 (mp0) REVERT: B 257 TRP cc_start: 0.8927 (m100) cc_final: 0.8709 (m100) REVERT: B 295 ILE cc_start: 0.8288 (mt) cc_final: 0.7888 (mt) REVERT: B 298 ASP cc_start: 0.7781 (p0) cc_final: 0.7421 (p0) REVERT: B 349 ILE cc_start: 0.8440 (mp) cc_final: 0.8227 (mm) REVERT: B 369 TYR cc_start: 0.8078 (m-10) cc_final: 0.7769 (m-10) REVERT: B 372 THR cc_start: 0.8527 (p) cc_final: 0.8091 (t) REVERT: B 373 MET cc_start: 0.8803 (mmp) cc_final: 0.8284 (mmp) REVERT: B 377 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 413 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 444 VAL cc_start: 0.8933 (t) cc_final: 0.8603 (m) REVERT: B 481 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6615 (t0) REVERT: B 518 ASN cc_start: 0.8160 (m-40) cc_final: 0.7678 (t0) REVERT: B 530 VAL cc_start: 0.8864 (t) cc_final: 0.8640 (p) REVERT: B 546 ASP cc_start: 0.7977 (t70) cc_final: 0.7741 (t0) REVERT: B 548 SER cc_start: 0.8489 (m) cc_final: 0.8144 (p) REVERT: B 566 VAL cc_start: 0.8809 (t) cc_final: 0.8419 (p) REVERT: D 82 VAL cc_start: 0.8951 (p) cc_final: 0.8594 (t) REVERT: D 149 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 151 ARG cc_start: 0.8628 (ptt180) cc_final: 0.6835 (ttt180) REVERT: D 271 PHE cc_start: 0.8902 (p90) cc_final: 0.8568 (p90) REVERT: D 304 PHE cc_start: 0.8441 (p90) cc_final: 0.8135 (p90) REVERT: D 344 PHE cc_start: 0.8391 (p90) cc_final: 0.7732 (p90) REVERT: D 362 ASN cc_start: 0.8314 (t0) cc_final: 0.7816 (t0) REVERT: D 364 SER cc_start: 0.8855 (m) cc_final: 0.8507 (p) REVERT: D 372 THR cc_start: 0.8616 (p) cc_final: 0.8133 (t) REVERT: D 373 MET cc_start: 0.8320 (mmm) cc_final: 0.7745 (mmm) REVERT: D 377 GLU cc_start: 0.8473 (tt0) cc_final: 0.7764 (tt0) REVERT: D 380 PHE cc_start: 0.7984 (m-80) cc_final: 0.7660 (m-80) REVERT: D 387 ASN cc_start: 0.8170 (t0) cc_final: 0.7571 (p0) REVERT: D 419 PHE cc_start: 0.8722 (t80) cc_final: 0.8518 (t80) REVERT: D 420 VAL cc_start: 0.8828 (t) cc_final: 0.8506 (m) REVERT: D 428 THR cc_start: 0.8653 (p) cc_final: 0.8385 (t) REVERT: D 466 VAL cc_start: 0.8594 (t) cc_final: 0.8287 (p) REVERT: D 474 ASN cc_start: 0.8207 (t0) cc_final: 0.7932 (t0) REVERT: D 511 GLN cc_start: 0.8762 (mt0) cc_final: 0.7824 (mt0) outliers start: 33 outliers final: 26 residues processed: 287 average time/residue: 0.2006 time to fit residues: 82.5152 Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.082746 restraints weight = 17295.516| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.48 r_work: 0.2830 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10319 Z= 0.283 Angle : 0.639 12.206 14166 Z= 0.326 Chirality : 0.051 0.170 1582 Planarity : 0.006 0.044 1869 Dihedral : 4.446 21.385 1422 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.32 % Allowed : 17.33 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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 (0.22), residues: 1320 helix: -0.57 (0.77), residues: 50 sheet: 0.07 (0.26), residues: 407 loop : -0.87 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 316 HIS 0.007 0.002 HIS C 179 PHE 0.020 0.002 PHE D 523 TYR 0.019 0.002 TYR D 91 ARG 0.005 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 292) hydrogen bonds : angle 6.46523 ( 741) covalent geometry : bond 0.00660 (10319) covalent geometry : angle 0.63865 (14166) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 1.136 Fit side-chains REVERT: A 79 THR cc_start: 0.8669 (m) cc_final: 0.8424 (p) REVERT: A 123 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8430 (m) REVERT: A 206 THR cc_start: 0.9010 (m) cc_final: 0.8660 (t) REVERT: B 74 TYR cc_start: 0.8858 (t80) cc_final: 0.8388 (t80) REVERT: B 75 ASN cc_start: 0.8536 (t0) cc_final: 0.8191 (t0) REVERT: B 143 GLU cc_start: 0.8269 (pp20) cc_final: 0.7930 (pp20) REVERT: B 149 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 151 ARG cc_start: 0.5824 (ptm160) cc_final: 0.5606 (ptm160) REVERT: B 168 ILE cc_start: 0.8455 (tp) cc_final: 0.8248 (tt) REVERT: B 177 MET cc_start: 0.8704 (mmm) cc_final: 0.8399 (mmp) REVERT: B 219 GLU cc_start: 0.7763 (mp0) cc_final: 0.7372 (mp0) REVERT: B 257 TRP cc_start: 0.8944 (m100) cc_final: 0.8733 (m100) REVERT: B 295 ILE cc_start: 0.8321 (mt) cc_final: 0.7952 (mt) REVERT: B 298 ASP cc_start: 0.7842 (p0) cc_final: 0.7469 (p0) REVERT: B 349 ILE cc_start: 0.8432 (mp) cc_final: 0.8224 (mm) REVERT: B 372 THR cc_start: 0.8548 (p) cc_final: 0.8177 (t) REVERT: B 377 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 413 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8315 (mm-40) REVERT: B 444 VAL cc_start: 0.8948 (t) cc_final: 0.8652 (m) REVERT: B 481 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6735 (t0) REVERT: B 518 ASN cc_start: 0.8254 (m-40) cc_final: 0.7889 (t0) REVERT: B 530 VAL cc_start: 0.8854 (t) cc_final: 0.8649 (p) REVERT: B 546 ASP cc_start: 0.8086 (t70) cc_final: 0.7815 (t0) REVERT: B 548 SER cc_start: 0.8499 (m) cc_final: 0.8161 (p) REVERT: B 566 VAL cc_start: 0.8924 (t) cc_final: 0.8565 (p) REVERT: D 82 VAL cc_start: 0.8926 (p) cc_final: 0.8549 (t) REVERT: D 149 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7703 (mm-30) REVERT: D 151 ARG cc_start: 0.8680 (ptt180) cc_final: 0.6897 (ttt180) REVERT: D 271 PHE cc_start: 0.8892 (p90) cc_final: 0.8541 (p90) REVERT: D 275 ASN cc_start: 0.8481 (t0) cc_final: 0.8210 (t0) REVERT: D 304 PHE cc_start: 0.8509 (p90) cc_final: 0.8136 (p90) REVERT: D 316 TRP cc_start: 0.8511 (t60) cc_final: 0.8222 (t60) REVERT: D 344 PHE cc_start: 0.8401 (p90) cc_final: 0.7754 (p90) REVERT: D 362 ASN cc_start: 0.8329 (t0) cc_final: 0.7888 (t0) REVERT: D 364 SER cc_start: 0.8846 (m) cc_final: 0.8505 (p) REVERT: D 372 THR cc_start: 0.8688 (p) cc_final: 0.8277 (t) REVERT: D 373 MET cc_start: 0.8350 (mmm) cc_final: 0.7885 (mmm) REVERT: D 377 GLU cc_start: 0.8457 (tt0) cc_final: 0.7870 (tt0) REVERT: D 387 ASN cc_start: 0.8188 (t0) cc_final: 0.7548 (p0) REVERT: D 420 VAL cc_start: 0.8878 (t) cc_final: 0.8538 (m) REVERT: D 428 THR cc_start: 0.8672 (p) cc_final: 0.8412 (t) REVERT: D 466 VAL cc_start: 0.8678 (t) cc_final: 0.8428 (p) REVERT: D 474 ASN cc_start: 0.8315 (t0) cc_final: 0.8098 (t0) REVERT: D 511 GLN cc_start: 0.8720 (mt0) cc_final: 0.7832 (mt0) REVERT: D 525 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 36 outliers final: 32 residues processed: 287 average time/residue: 0.2732 time to fit residues: 113.3796 Evaluate side-chains 301 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 119 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.085854 restraints weight = 17291.934| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.51 r_work: 0.2896 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10319 Z= 0.096 Angle : 0.552 12.382 14166 Z= 0.272 Chirality : 0.047 0.170 1582 Planarity : 0.005 0.038 1869 Dihedral : 4.011 18.266 1422 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 18.34 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1320 helix: -0.08 (0.82), residues: 50 sheet: 0.29 (0.27), residues: 374 loop : -0.80 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 316 HIS 0.004 0.001 HIS D 277 PHE 0.020 0.001 PHE D 523 TYR 0.014 0.001 TYR B 369 ARG 0.003 0.000 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 292) hydrogen bonds : angle 6.16412 ( 741) covalent geometry : bond 0.00222 (10319) covalent geometry : angle 0.55207 (14166) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 1.188 Fit side-chains REVERT: A 113 TRP cc_start: 0.8933 (p-90) cc_final: 0.8216 (p-90) REVERT: A 123 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8498 (m) REVERT: A 206 THR cc_start: 0.8976 (m) cc_final: 0.8630 (t) REVERT: B 74 TYR cc_start: 0.8808 (t80) cc_final: 0.8322 (t80) REVERT: B 75 ASN cc_start: 0.8412 (t0) cc_final: 0.8147 (t0) REVERT: B 106 LEU cc_start: 0.8202 (mt) cc_final: 0.7832 (mt) REVERT: B 143 GLU cc_start: 0.8263 (pp20) cc_final: 0.7928 (pp20) REVERT: B 149 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 151 ARG cc_start: 0.6087 (ptm160) cc_final: 0.5761 (ptm160) REVERT: B 177 MET cc_start: 0.8682 (mmm) cc_final: 0.8405 (mmp) REVERT: B 219 GLU cc_start: 0.7709 (mp0) cc_final: 0.7333 (mp0) REVERT: B 257 TRP cc_start: 0.8876 (m100) cc_final: 0.8672 (m100) REVERT: B 295 ILE cc_start: 0.8262 (mt) cc_final: 0.7872 (mt) REVERT: B 338 ASP cc_start: 0.8289 (p0) cc_final: 0.7838 (p0) REVERT: B 339 MET cc_start: 0.8272 (mtp) cc_final: 0.7966 (mtp) REVERT: B 349 ILE cc_start: 0.8425 (mp) cc_final: 0.8208 (mm) REVERT: B 372 THR cc_start: 0.8514 (p) cc_final: 0.8089 (t) REVERT: B 373 MET cc_start: 0.8765 (mmp) cc_final: 0.8288 (mmp) REVERT: B 377 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 413 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8288 (mm-40) REVERT: B 444 VAL cc_start: 0.8943 (t) cc_final: 0.8652 (m) REVERT: B 481 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6758 (t0) REVERT: B 518 ASN cc_start: 0.8115 (m-40) cc_final: 0.7706 (t0) REVERT: B 530 VAL cc_start: 0.8931 (t) cc_final: 0.8701 (p) REVERT: B 546 ASP cc_start: 0.7979 (t70) cc_final: 0.7743 (t0) REVERT: B 548 SER cc_start: 0.8506 (m) cc_final: 0.8175 (p) REVERT: B 566 VAL cc_start: 0.8805 (t) cc_final: 0.8431 (p) REVERT: C 72 PHE cc_start: 0.8314 (m-80) cc_final: 0.7985 (m-80) REVERT: C 99 ASN cc_start: 0.8078 (m-40) cc_final: 0.7871 (m-40) REVERT: D 108 GLN cc_start: 0.8776 (tt0) cc_final: 0.8487 (tt0) REVERT: D 149 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7649 (mm-30) REVERT: D 151 ARG cc_start: 0.8623 (ptt180) cc_final: 0.6845 (ttt180) REVERT: D 271 PHE cc_start: 0.8884 (p90) cc_final: 0.8473 (p90) REVERT: D 275 ASN cc_start: 0.8571 (t0) cc_final: 0.8340 (t0) REVERT: D 304 PHE cc_start: 0.8465 (p90) cc_final: 0.8128 (p90) REVERT: D 362 ASN cc_start: 0.8322 (t0) cc_final: 0.7844 (t0) REVERT: D 364 SER cc_start: 0.8854 (m) cc_final: 0.8512 (p) REVERT: D 372 THR cc_start: 0.8639 (p) cc_final: 0.8246 (t) REVERT: D 373 MET cc_start: 0.8318 (mmm) cc_final: 0.7892 (mmm) REVERT: D 377 GLU cc_start: 0.8465 (tt0) cc_final: 0.7753 (tt0) REVERT: D 380 PHE cc_start: 0.7942 (m-80) cc_final: 0.7634 (m-80) REVERT: D 387 ASN cc_start: 0.8124 (t0) cc_final: 0.7565 (p0) REVERT: D 420 VAL cc_start: 0.8722 (t) cc_final: 0.8434 (m) REVERT: D 428 THR cc_start: 0.8663 (p) cc_final: 0.8392 (t) REVERT: D 466 VAL cc_start: 0.8590 (t) cc_final: 0.8290 (p) REVERT: D 474 ASN cc_start: 0.8131 (t0) cc_final: 0.7894 (t0) REVERT: D 511 GLN cc_start: 0.8745 (mt0) cc_final: 0.7861 (mt0) REVERT: D 525 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7587 (mt-10) outliers start: 29 outliers final: 24 residues processed: 286 average time/residue: 0.2231 time to fit residues: 92.0015 Evaluate side-chains 300 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN D 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.086195 restraints weight = 17128.212| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.49 r_work: 0.2874 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10319 Z= 0.107 Angle : 0.559 12.281 14166 Z= 0.275 Chirality : 0.047 0.195 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.956 17.227 1422 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 18.80 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.56 (0.22), residues: 1320 helix: 0.09 (0.83), residues: 50 sheet: 0.33 (0.27), residues: 382 loop : -0.73 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 316 HIS 0.003 0.001 HIS D 277 PHE 0.020 0.001 PHE D 523 TYR 0.013 0.001 TYR B 369 ARG 0.004 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 292) hydrogen bonds : angle 6.09435 ( 741) covalent geometry : bond 0.00253 (10319) covalent geometry : angle 0.55887 (14166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5260.47 seconds wall clock time: 92 minutes 46.45 seconds (5566.45 seconds total)