Starting phenix.real_space_refine on Thu Jan 16 18:08:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jji_61528/01_2025/9jji_61528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jji_61528/01_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_61528/01_2025/9jji_61528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jji_61528/01_2025/9jji_61528.map" model { file = "/net/cci-nas-00/data/ceres_data/9jji_61528/01_2025/9jji_61528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jji_61528/01_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-5571/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: 6.08, per 1000 atoms: 0.61 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: 2.56 Conformation dependent library (CDL) restraints added in 1.4 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: 1.45 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: 3.48 Time building geometry restraints manager: 2.94 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: 0.090 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.950 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- 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= 0.301 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 *********************** 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 : 1.009 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: 0.2248 time to fit residues: 92.2439 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 : 1.051 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.099042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.085918 restraints weight = 16698.582| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.33 r_work: 0.2854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1531 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= 0.244 Angle : 0.581 7.363 14166 Z= 0.296 Chirality : 0.048 0.175 1582 Planarity : 0.005 0.042 1869 Dihedral : 4.188 18.285 1422 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.55 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 *********************** 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 : 1.023 Fit side-chains REVERT: A 113 TRP cc_start: 0.8965 (p-90) cc_final: 0.8283 (p-90) REVERT: A 128 VAL cc_start: 0.8494 (m) cc_final: 0.8217 (t) REVERT: A 206 THR cc_start: 0.8904 (m) cc_final: 0.8326 (p) REVERT: A 225 MET cc_start: 0.7537 (mtt) cc_final: 0.7326 (mtt) REVERT: B 74 TYR cc_start: 0.8804 (t80) cc_final: 0.8225 (t80) REVERT: B 143 GLU cc_start: 0.8257 (pp20) cc_final: 0.7921 (pp20) REVERT: B 161 ARG cc_start: 0.8627 (ptt-90) cc_final: 0.8381 (ptt180) REVERT: B 227 ARG cc_start: 0.8546 (ptt180) cc_final: 0.8332 (ptt-90) REVERT: B 262 VAL cc_start: 0.9030 (m) cc_final: 0.8672 (t) REVERT: B 295 ILE cc_start: 0.8209 (mt) cc_final: 0.7885 (mt) REVERT: B 298 ASP cc_start: 0.7433 (p0) cc_final: 0.7066 (p0) REVERT: B 369 TYR cc_start: 0.8025 (m-10) cc_final: 0.7767 (m-10) REVERT: B 398 GLN cc_start: 0.8358 (mt0) cc_final: 0.8052 (mt0) REVERT: B 413 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8373 (mm-40) REVERT: B 444 VAL cc_start: 0.8711 (t) cc_final: 0.8335 (m) REVERT: B 455 ILE cc_start: 0.8449 (tp) cc_final: 0.8144 (pt) REVERT: B 530 VAL cc_start: 0.8830 (t) cc_final: 0.8610 (p) REVERT: B 546 ASP cc_start: 0.7919 (t70) cc_final: 0.7600 (t0) REVERT: B 548 SER cc_start: 0.8649 (m) cc_final: 0.8326 (p) REVERT: B 566 VAL cc_start: 0.8839 (t) cc_final: 0.8614 (m) REVERT: C 99 ASN cc_start: 0.8087 (m-40) cc_final: 0.7785 (m110) REVERT: D 151 ARG cc_start: 0.8646 (ptt180) cc_final: 0.6944 (ttt180) REVERT: D 152 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7527 (mm-40) REVERT: D 210 GLN cc_start: 0.8382 (mm110) cc_final: 0.8083 (mm110) REVERT: D 213 VAL cc_start: 0.7905 (t) cc_final: 0.7681 (m) REVERT: D 271 PHE cc_start: 0.8874 (p90) cc_final: 0.8496 (p90) REVERT: D 344 PHE cc_start: 0.8373 (p90) cc_final: 0.8122 (p90) REVERT: D 362 ASN cc_start: 0.8240 (t0) cc_final: 0.7750 (t0) REVERT: D 364 SER cc_start: 0.8840 (m) cc_final: 0.8491 (p) REVERT: D 373 MET cc_start: 0.8190 (mmm) cc_final: 0.7732 (mmm) REVERT: D 377 GLU cc_start: 0.8460 (tt0) cc_final: 0.7858 (tt0) REVERT: D 387 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.6973 (p0) REVERT: D 428 THR cc_start: 0.8559 (p) cc_final: 0.8245 (t) REVERT: D 466 VAL cc_start: 0.8674 (t) cc_final: 0.8339 (p) REVERT: D 511 GLN cc_start: 0.8732 (mt0) cc_final: 0.8459 (mt0) REVERT: D 514 VAL cc_start: 0.8645 (t) cc_final: 0.8410 (m) REVERT: D 523 PHE cc_start: 0.8255 (p90) cc_final: 0.7942 (p90) REVERT: D 549 ASP cc_start: 0.8067 (m-30) cc_final: 0.7843 (m-30) REVERT: D 566 VAL cc_start: 0.8488 (t) cc_final: 0.8225 (t) outliers start: 16 outliers final: 15 residues processed: 264 average time/residue: 0.2105 time to fit residues: 79.6131 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 : 1.117 ------------------------------------------------------------------------------- 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: 0.3980 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.095825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.082510 restraints weight = 17416.188| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.50 r_work: 0.2839 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1936 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= 0.217 Angle : 0.545 6.810 14166 Z= 0.276 Chirality : 0.047 0.150 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.054 17.283 1422 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.49 % Allowed : 11.43 % Favored : 86.08 % 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: -0.96 (0.79), residues: 50 sheet: 0.47 (0.25), residues: 406 loop : -0.71 (0.19), residues: 864 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 0.013 0.001 TYR D 91 ARG 0.003 0.000 ARG C 161 *********************** 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 279 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8968 (p-90) cc_final: 0.8253 (p-90) REVERT: A 128 VAL cc_start: 0.8420 (m) cc_final: 0.8175 (t) REVERT: A 206 THR cc_start: 0.8890 (m) cc_final: 0.8303 (p) REVERT: A 225 MET cc_start: 0.7575 (mtt) cc_final: 0.7372 (mtt) REVERT: B 74 TYR cc_start: 0.8845 (t80) cc_final: 0.8255 (t80) REVERT: B 143 GLU cc_start: 0.8265 (pp20) cc_final: 0.7924 (pp20) REVERT: B 262 VAL cc_start: 0.8983 (m) cc_final: 0.8731 (t) REVERT: B 295 ILE cc_start: 0.8211 (mt) cc_final: 0.7891 (mt) REVERT: B 298 ASP cc_start: 0.7572 (p0) cc_final: 0.7213 (p0) REVERT: B 372 THR cc_start: 0.8599 (p) cc_final: 0.8067 (t) REVERT: B 387 ASN cc_start: 0.7101 (t0) cc_final: 0.6546 (t0) REVERT: B 398 GLN cc_start: 0.8364 (mt0) cc_final: 0.8057 (mt0) REVERT: B 413 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8350 (mm-40) REVERT: B 444 VAL cc_start: 0.8780 (t) cc_final: 0.8424 (m) REVERT: B 530 VAL cc_start: 0.8890 (t) cc_final: 0.8666 (p) REVERT: B 546 ASP cc_start: 0.7916 (t70) cc_final: 0.7648 (t0) REVERT: B 548 SER cc_start: 0.8664 (m) cc_final: 0.8285 (p) REVERT: B 559 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (tpp80) REVERT: B 566 VAL cc_start: 0.8862 (t) cc_final: 0.8638 (m) REVERT: C 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7739 (m110) REVERT: C 129 PHE cc_start: 0.8621 (m-80) cc_final: 0.7907 (m-80) REVERT: C 176 ASN cc_start: 0.8510 (m-40) cc_final: 0.8267 (m-40) REVERT: C 177 MET cc_start: 0.7816 (mmt) cc_final: 0.7171 (mmt) REVERT: D 151 ARG cc_start: 0.8675 (ptt180) cc_final: 0.7179 (ptm160) REVERT: D 177 MET cc_start: 0.7965 (mmm) cc_final: 0.7171 (mmt) REVERT: D 210 GLN cc_start: 0.8365 (mm110) cc_final: 0.8044 (mm110) REVERT: D 213 VAL cc_start: 0.7927 (t) cc_final: 0.7638 (m) REVERT: D 271 PHE cc_start: 0.8913 (p90) cc_final: 0.8622 (p90) REVERT: D 344 PHE cc_start: 0.8391 (p90) cc_final: 0.8059 (p90) REVERT: D 362 ASN cc_start: 0.8328 (t0) cc_final: 0.7769 (t0) REVERT: D 364 SER cc_start: 0.8874 (m) cc_final: 0.8548 (p) REVERT: D 373 MET cc_start: 0.8244 (mmm) cc_final: 0.7744 (mmm) REVERT: D 377 GLU cc_start: 0.8510 (tt0) cc_final: 0.7864 (tt0) REVERT: D 380 PHE cc_start: 0.8146 (m-80) cc_final: 0.7800 (m-80) REVERT: D 387 ASN cc_start: 0.8036 (t0) cc_final: 0.7178 (p0) REVERT: D 420 VAL cc_start: 0.8762 (t) cc_final: 0.8420 (m) REVERT: D 428 THR cc_start: 0.8595 (p) cc_final: 0.8341 (t) REVERT: D 466 VAL cc_start: 0.8635 (t) cc_final: 0.8320 (p) REVERT: D 511 GLN cc_start: 0.8761 (mt0) cc_final: 0.7835 (mt0) REVERT: D 514 VAL cc_start: 0.8691 (t) cc_final: 0.8412 (m) REVERT: D 523 PHE cc_start: 0.8164 (p90) cc_final: 0.7850 (p90) REVERT: D 566 VAL cc_start: 0.8479 (t) cc_final: 0.7858 (m) outliers start: 27 outliers final: 21 residues processed: 266 average time/residue: 0.2161 time to fit residues: 81.9711 Evaluate side-chains 267 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 125 optimal weight: 0.0370 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 82 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.083948 restraints weight = 17085.516| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.43 r_work: 0.2821 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10319 Z= 0.315 Angle : 0.581 7.471 14166 Z= 0.297 Chirality : 0.048 0.149 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.266 18.155 1422 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.23 % Allowed : 12.63 % Favored : 84.15 % 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: -0.67 (0.22), residues: 1320 helix: -1.04 (0.77), residues: 50 sheet: 0.23 (0.25), residues: 412 loop : -0.75 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 68 HIS 0.006 0.002 HIS C 179 PHE 0.015 0.002 PHE D 223 TYR 0.016 0.002 TYR D 91 ARG 0.003 0.000 ARG A 151 *********************** 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 302 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 206 THR cc_start: 0.8935 (m) cc_final: 0.8499 (t) REVERT: B 74 TYR cc_start: 0.8853 (t80) cc_final: 0.8316 (t80) REVERT: B 75 ASN cc_start: 0.8510 (t0) cc_final: 0.8171 (t0) REVERT: B 143 GLU cc_start: 0.8212 (pp20) cc_final: 0.7914 (pp20) REVERT: B 149 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7060 (mm-30) REVERT: B 219 GLU cc_start: 0.7733 (mp0) cc_final: 0.7340 (mp0) REVERT: B 257 TRP cc_start: 0.8972 (m100) cc_final: 0.8754 (m100) REVERT: B 262 VAL cc_start: 0.9000 (m) cc_final: 0.8771 (t) REVERT: B 295 ILE cc_start: 0.8305 (mt) cc_final: 0.7947 (mt) REVERT: B 298 ASP cc_start: 0.7666 (p0) cc_final: 0.7255 (p0) REVERT: B 349 ILE cc_start: 0.8430 (mp) cc_final: 0.8210 (mm) REVERT: B 372 THR cc_start: 0.8568 (p) cc_final: 0.8110 (t) REVERT: B 377 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 387 ASN cc_start: 0.7241 (t0) cc_final: 0.6750 (t0) REVERT: B 398 GLN cc_start: 0.8354 (mt0) cc_final: 0.8073 (mt0) REVERT: B 413 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8366 (mm-40) REVERT: B 444 VAL cc_start: 0.8854 (t) cc_final: 0.8502 (m) REVERT: B 530 VAL cc_start: 0.8948 (t) cc_final: 0.8727 (p) REVERT: B 546 ASP cc_start: 0.7911 (t70) cc_final: 0.7648 (t0) REVERT: B 548 SER cc_start: 0.8623 (m) cc_final: 0.8254 (p) REVERT: B 559 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7890 (tpp80) REVERT: B 566 VAL cc_start: 0.8900 (t) cc_final: 0.8589 (m) REVERT: D 82 VAL cc_start: 0.8979 (p) cc_final: 0.8614 (t) REVERT: D 151 ARG cc_start: 0.8693 (ptt180) cc_final: 0.7153 (ptm160) REVERT: D 271 PHE cc_start: 0.8892 (p90) cc_final: 0.8528 (p90) REVERT: D 275 ASN cc_start: 0.8497 (t0) cc_final: 0.8285 (t0) REVERT: D 316 TRP cc_start: 0.8542 (t60) cc_final: 0.8163 (t60) REVERT: D 344 PHE cc_start: 0.8401 (p90) cc_final: 0.7931 (p90) REVERT: D 362 ASN cc_start: 0.8357 (t0) cc_final: 0.7807 (t0) REVERT: D 364 SER cc_start: 0.8857 (m) cc_final: 0.8540 (p) REVERT: D 371 THR cc_start: 0.8331 (p) cc_final: 0.7689 (t) REVERT: D 373 MET cc_start: 0.8217 (mmm) cc_final: 0.7741 (mmm) REVERT: D 377 GLU cc_start: 0.8464 (tt0) cc_final: 0.7765 (tt0) REVERT: D 387 ASN cc_start: 0.8212 (t0) cc_final: 0.7664 (p0) REVERT: D 428 THR cc_start: 0.8662 (p) cc_final: 0.8404 (t) REVERT: D 466 VAL cc_start: 0.8651 (t) cc_final: 0.8352 (p) REVERT: D 511 GLN cc_start: 0.8769 (mt0) cc_final: 0.7813 (mt0) REVERT: D 514 VAL cc_start: 0.8701 (t) cc_final: 0.8397 (m) REVERT: D 523 PHE cc_start: 0.8182 (p90) cc_final: 0.7909 (p90) REVERT: D 566 VAL cc_start: 0.8561 (t) cc_final: 0.8050 (m) outliers start: 35 outliers final: 30 residues processed: 282 average time/residue: 0.2077 time to fit residues: 83.6427 Evaluate side-chains 293 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 507 LEU 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: 0.9990 chunk 110 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.099270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.086166 restraints weight = 17126.644| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.45 r_work: 0.2868 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2473 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= 0.159 Angle : 0.521 8.838 14166 Z= 0.261 Chirality : 0.046 0.144 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.958 16.927 1422 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.86 % Allowed : 14.19 % Favored : 82.95 % 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: -0.57 (0.22), residues: 1320 helix: -0.63 (0.80), residues: 50 sheet: 0.39 (0.25), residues: 398 loop : -0.74 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 68 HIS 0.003 0.001 HIS C 179 PHE 0.011 0.001 PHE A 221 TYR 0.012 0.001 TYR D 91 ARG 0.002 0.000 ARG A 151 *********************** 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 290 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8960 (p-90) cc_final: 0.8301 (p-90) REVERT: A 206 THR cc_start: 0.8927 (m) cc_final: 0.8476 (t) REVERT: B 74 TYR cc_start: 0.8810 (t80) cc_final: 0.8270 (t80) REVERT: B 75 ASN cc_start: 0.8445 (t0) cc_final: 0.8148 (t0) REVERT: B 151 ARG cc_start: 0.5815 (ptm160) cc_final: 0.5594 (ptm160) REVERT: B 177 MET cc_start: 0.8699 (mmm) cc_final: 0.8402 (mmp) REVERT: B 257 TRP cc_start: 0.8930 (m100) cc_final: 0.8693 (m100) REVERT: B 295 ILE cc_start: 0.8272 (mt) cc_final: 0.7895 (mt) REVERT: B 298 ASP cc_start: 0.7652 (p0) cc_final: 0.7258 (p0) REVERT: B 349 ILE cc_start: 0.8429 (mp) cc_final: 0.8211 (mm) REVERT: B 372 THR cc_start: 0.8556 (p) cc_final: 0.8109 (t) REVERT: B 373 MET cc_start: 0.8847 (mmp) cc_final: 0.8366 (mmp) REVERT: B 413 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8358 (mm-40) REVERT: B 444 VAL cc_start: 0.8837 (t) cc_final: 0.8498 (m) REVERT: B 481 ASN cc_start: 0.6938 (OUTLIER) cc_final: 0.6687 (t160) REVERT: B 530 VAL cc_start: 0.8867 (t) cc_final: 0.8651 (p) REVERT: B 546 ASP cc_start: 0.7886 (t70) cc_final: 0.7655 (t0) REVERT: B 548 SER cc_start: 0.8593 (m) cc_final: 0.8214 (p) REVERT: B 566 VAL cc_start: 0.8848 (t) cc_final: 0.8637 (m) REVERT: D 151 ARG cc_start: 0.8656 (ptt180) cc_final: 0.6923 (ttt180) REVERT: D 177 MET cc_start: 0.7916 (mmm) cc_final: 0.7697 (mmp) REVERT: D 271 PHE cc_start: 0.8902 (p90) cc_final: 0.8559 (p90) REVERT: D 344 PHE cc_start: 0.8405 (p90) cc_final: 0.7834 (p90) REVERT: D 362 ASN cc_start: 0.8325 (t0) cc_final: 0.7835 (t0) REVERT: D 364 SER cc_start: 0.8867 (m) cc_final: 0.8547 (p) REVERT: D 373 MET cc_start: 0.8225 (mmm) cc_final: 0.7690 (mmm) REVERT: D 377 GLU cc_start: 0.8473 (tt0) cc_final: 0.7790 (tt0) REVERT: D 380 PHE cc_start: 0.8057 (m-80) cc_final: 0.7775 (m-80) REVERT: D 387 ASN cc_start: 0.8102 (t0) cc_final: 0.7601 (p0) REVERT: D 428 THR cc_start: 0.8663 (p) cc_final: 0.8400 (t) REVERT: D 466 VAL cc_start: 0.8593 (t) cc_final: 0.8253 (p) REVERT: D 511 GLN cc_start: 0.8760 (mt0) cc_final: 0.7887 (mt0) REVERT: D 525 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7451 (mt-10) outliers start: 31 outliers final: 23 residues processed: 272 average time/residue: 0.2059 time to fit residues: 80.1350 Evaluate side-chains 277 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 260 GLU 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 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 467 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: 0.0770 chunk 107 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 119 optimal weight: 0.0770 chunk 117 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.8302 ------------------------------------------------------------------------------- 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** C 99 ASN D 265 GLN D 412 ASN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.082502 restraints weight = 17348.621| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.54 r_work: 0.2817 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10319 Z= 0.256 Angle : 0.557 9.509 14166 Z= 0.280 Chirality : 0.048 0.181 1582 Planarity : 0.005 0.039 1869 Dihedral : 4.076 17.633 1422 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.59 % Allowed : 14.75 % Favored : 81.66 % 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: -0.62 (0.22), residues: 1320 helix: -0.63 (0.79), residues: 50 sheet: 0.31 (0.26), residues: 398 loop : -0.76 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 68 HIS 0.005 0.001 HIS C 179 PHE 0.022 0.001 PHE D 523 TYR 0.016 0.001 TYR D 91 ARG 0.002 0.000 ARG A 151 *********************** 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 308 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8976 (p-90) cc_final: 0.8237 (p-90) REVERT: A 206 THR cc_start: 0.8983 (m) cc_final: 0.8575 (t) REVERT: B 74 TYR cc_start: 0.8824 (t80) cc_final: 0.8284 (t80) REVERT: B 75 ASN cc_start: 0.8479 (t0) cc_final: 0.8165 (t0) REVERT: B 143 GLU cc_start: 0.8270 (pp20) cc_final: 0.7937 (pp20) REVERT: B 149 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7006 (mm-30) REVERT: B 151 ARG cc_start: 0.5790 (ptm160) cc_final: 0.5554 (ptm160) REVERT: B 177 MET cc_start: 0.8669 (mmm) cc_final: 0.8354 (mmp) REVERT: B 219 GLU cc_start: 0.7754 (mp0) cc_final: 0.7355 (mp0) REVERT: B 257 TRP cc_start: 0.8969 (m100) cc_final: 0.8720 (m100) REVERT: B 295 ILE cc_start: 0.8298 (mt) cc_final: 0.7911 (mt) REVERT: B 298 ASP cc_start: 0.7753 (p0) cc_final: 0.7367 (p0) REVERT: B 349 ILE cc_start: 0.8444 (mp) cc_final: 0.8215 (mm) REVERT: B 369 TYR cc_start: 0.8122 (m-10) cc_final: 0.7794 (m-10) REVERT: B 372 THR cc_start: 0.8563 (p) cc_final: 0.8114 (t) REVERT: B 373 MET cc_start: 0.8795 (mmp) cc_final: 0.8277 (mmp) REVERT: B 377 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 413 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8367 (mm-40) REVERT: B 444 VAL cc_start: 0.8876 (t) cc_final: 0.8559 (m) REVERT: B 481 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6709 (t160) REVERT: B 530 VAL cc_start: 0.8861 (t) cc_final: 0.8641 (p) REVERT: B 546 ASP cc_start: 0.7899 (t70) cc_final: 0.7662 (t0) REVERT: B 548 SER cc_start: 0.8551 (m) cc_final: 0.8237 (p) REVERT: B 566 VAL cc_start: 0.8866 (t) cc_final: 0.8639 (m) REVERT: D 149 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 151 ARG cc_start: 0.8638 (ptt180) cc_final: 0.6824 (ttt180) REVERT: D 177 MET cc_start: 0.7913 (mmm) cc_final: 0.7712 (mmp) REVERT: D 271 PHE cc_start: 0.8915 (p90) cc_final: 0.8543 (p90) REVERT: D 275 ASN cc_start: 0.8496 (t0) cc_final: 0.8263 (t0) REVERT: D 304 PHE cc_start: 0.8469 (p90) cc_final: 0.8173 (p90) REVERT: D 344 PHE cc_start: 0.8444 (p90) cc_final: 0.7867 (p90) REVERT: D 362 ASN cc_start: 0.8331 (t0) cc_final: 0.7808 (t0) REVERT: D 364 SER cc_start: 0.8858 (m) cc_final: 0.8511 (p) REVERT: D 372 THR cc_start: 0.8606 (p) cc_final: 0.8095 (t) REVERT: D 373 MET cc_start: 0.8291 (mmm) cc_final: 0.7910 (mmm) REVERT: D 377 GLU cc_start: 0.8484 (tt0) cc_final: 0.7751 (tt0) REVERT: D 380 PHE cc_start: 0.8093 (m-80) cc_final: 0.7777 (m-80) REVERT: D 387 ASN cc_start: 0.8146 (t0) cc_final: 0.7464 (p0) REVERT: D 428 THR cc_start: 0.8665 (p) cc_final: 0.8391 (t) REVERT: D 466 VAL cc_start: 0.8630 (t) cc_final: 0.8321 (p) REVERT: D 511 GLN cc_start: 0.8764 (mt0) cc_final: 0.7814 (mt0) REVERT: D 525 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7700 (mt-10) outliers start: 39 outliers final: 31 residues processed: 289 average time/residue: 0.2161 time to fit residues: 89.8288 Evaluate side-chains 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 C residue 206 THR 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 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 507 LEU 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: 10.0000 chunk 104 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN C 99 ASN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.084328 restraints weight = 17354.253| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.51 r_work: 0.2881 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10319 Z= 0.180 Angle : 0.533 10.195 14166 Z= 0.266 Chirality : 0.047 0.139 1582 Planarity : 0.005 0.038 1869 Dihedral : 3.958 19.817 1422 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.59 % Allowed : 16.50 % Favored : 79.91 % 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: -0.62 (0.22), residues: 1320 helix: -0.41 (0.81), residues: 50 sheet: 0.33 (0.26), residues: 376 loop : -0.76 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 68 HIS 0.004 0.001 HIS D 277 PHE 0.022 0.001 PHE D 523 TYR 0.012 0.001 TYR D 91 ARG 0.002 0.000 ARG C 161 *********************** 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: 39 poor density : 268 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8938 (p-90) cc_final: 0.8216 (p-90) REVERT: A 123 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8508 (m) REVERT: A 206 THR cc_start: 0.8974 (m) cc_final: 0.8562 (t) REVERT: B 74 TYR cc_start: 0.8833 (t80) cc_final: 0.8285 (t80) REVERT: B 75 ASN cc_start: 0.8453 (t0) cc_final: 0.8164 (t0) REVERT: B 143 GLU cc_start: 0.8266 (pp20) cc_final: 0.7917 (pp20) REVERT: B 149 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 177 MET cc_start: 0.8721 (mmm) cc_final: 0.8415 (mmp) REVERT: B 219 GLU cc_start: 0.7717 (mp0) cc_final: 0.7335 (mp0) REVERT: B 257 TRP cc_start: 0.8932 (m100) cc_final: 0.8682 (m100) REVERT: B 295 ILE cc_start: 0.8305 (mt) cc_final: 0.7947 (mt) REVERT: B 298 ASP cc_start: 0.7745 (p0) cc_final: 0.7369 (p0) REVERT: B 299 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7409 (mmm-85) REVERT: B 349 ILE cc_start: 0.8455 (mp) cc_final: 0.8230 (mm) REVERT: B 369 TYR cc_start: 0.8048 (m-10) cc_final: 0.7761 (m-10) REVERT: B 372 THR cc_start: 0.8562 (p) cc_final: 0.8121 (t) REVERT: B 373 MET cc_start: 0.8791 (mmp) cc_final: 0.8298 (mmp) REVERT: B 377 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 413 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8345 (mm-40) REVERT: B 444 VAL cc_start: 0.8867 (t) cc_final: 0.8555 (m) REVERT: B 481 ASN cc_start: 0.7054 (OUTLIER) cc_final: 0.6692 (t0) REVERT: B 518 ASN cc_start: 0.8154 (m-40) cc_final: 0.7701 (t0) REVERT: B 530 VAL cc_start: 0.8866 (t) cc_final: 0.8649 (p) REVERT: B 546 ASP cc_start: 0.7972 (t70) cc_final: 0.7747 (t0) REVERT: B 548 SER cc_start: 0.8584 (m) cc_final: 0.8193 (p) REVERT: B 566 VAL cc_start: 0.8859 (t) cc_final: 0.8485 (p) REVERT: C 99 ASN cc_start: 0.8012 (m-40) cc_final: 0.7666 (m110) REVERT: D 149 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 151 ARG cc_start: 0.8653 (ptt180) cc_final: 0.6845 (ttt180) REVERT: D 271 PHE cc_start: 0.8895 (p90) cc_final: 0.8546 (p90) REVERT: D 304 PHE cc_start: 0.8470 (p90) cc_final: 0.8184 (p90) REVERT: D 344 PHE cc_start: 0.8409 (p90) cc_final: 0.7783 (p90) REVERT: D 362 ASN cc_start: 0.8320 (t0) cc_final: 0.7837 (t0) REVERT: D 364 SER cc_start: 0.8860 (m) cc_final: 0.8514 (p) REVERT: D 372 THR cc_start: 0.8585 (p) cc_final: 0.8100 (t) REVERT: D 373 MET cc_start: 0.8247 (mmm) cc_final: 0.7685 (mmm) REVERT: D 377 GLU cc_start: 0.8470 (tt0) cc_final: 0.7777 (tt0) REVERT: D 380 PHE cc_start: 0.8008 (m-80) cc_final: 0.7729 (m-80) REVERT: D 387 ASN cc_start: 0.8170 (t0) cc_final: 0.7442 (p0) REVERT: D 428 THR cc_start: 0.8666 (p) cc_final: 0.8402 (t) REVERT: D 458 ASN cc_start: 0.8069 (m-40) cc_final: 0.7834 (m-40) REVERT: D 466 VAL cc_start: 0.8601 (t) cc_final: 0.8279 (p) REVERT: D 511 GLN cc_start: 0.8761 (mt0) cc_final: 0.7863 (mt0) outliers start: 39 outliers final: 30 residues processed: 289 average time/residue: 0.2210 time to fit residues: 91.3407 Evaluate side-chains 299 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain B residue 481 ASN 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 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 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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** D 95 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 = 0.3107 r_free = 0.3107 target = 0.095096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.082108 restraints weight = 17331.387| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.50 r_work: 0.2821 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10319 Z= 0.403 Angle : 0.618 10.697 14166 Z= 0.317 Chirality : 0.050 0.155 1582 Planarity : 0.006 0.041 1869 Dihedral : 4.423 20.881 1422 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.96 % Allowed : 16.77 % Favored : 79.26 % 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: -0.84 (0.21), residues: 1320 helix: -0.73 (0.76), residues: 50 sheet: 0.08 (0.26), residues: 385 loop : -0.86 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 68 HIS 0.006 0.002 HIS C 179 PHE 0.023 0.002 PHE D 523 TYR 0.018 0.002 TYR D 91 ARG 0.007 0.001 ARG C 216 *********************** 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 310 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 1.118 Fit side-chains REVERT: A 123 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (m) REVERT: A 206 THR cc_start: 0.8975 (m) cc_final: 0.8637 (t) REVERT: B 74 TYR cc_start: 0.8861 (t80) cc_final: 0.8374 (t80) REVERT: B 75 ASN cc_start: 0.8519 (t0) cc_final: 0.8173 (t0) REVERT: B 143 GLU cc_start: 0.8278 (pp20) cc_final: 0.7904 (pp20) REVERT: B 149 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 177 MET cc_start: 0.8687 (mmm) cc_final: 0.8354 (mmp) REVERT: B 219 GLU cc_start: 0.7752 (mp0) cc_final: 0.7368 (mp0) REVERT: B 257 TRP cc_start: 0.8956 (m100) cc_final: 0.8710 (m100) REVERT: B 295 ILE cc_start: 0.8329 (mt) cc_final: 0.7935 (mt) REVERT: B 298 ASP cc_start: 0.7824 (p0) cc_final: 0.7461 (p0) REVERT: B 349 ILE cc_start: 0.8435 (mp) cc_final: 0.8224 (mm) REVERT: B 372 THR cc_start: 0.8558 (p) cc_final: 0.8180 (t) REVERT: B 377 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 413 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8321 (mm-40) REVERT: B 444 VAL cc_start: 0.8940 (t) cc_final: 0.8629 (m) REVERT: B 481 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6713 (t0) REVERT: B 530 VAL cc_start: 0.8845 (t) cc_final: 0.8638 (p) REVERT: B 546 ASP cc_start: 0.8066 (t70) cc_final: 0.7803 (t0) REVERT: B 548 SER cc_start: 0.8488 (m) cc_final: 0.8130 (p) REVERT: B 566 VAL cc_start: 0.8908 (t) cc_final: 0.8538 (p) REVERT: C 99 ASN cc_start: 0.8308 (m-40) cc_final: 0.7992 (m-40) REVERT: D 82 VAL cc_start: 0.9006 (p) cc_final: 0.8653 (t) REVERT: D 149 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7663 (mm-30) REVERT: D 151 ARG cc_start: 0.8669 (ptt180) cc_final: 0.6871 (ttt180) REVERT: D 271 PHE cc_start: 0.8901 (p90) cc_final: 0.8557 (p90) REVERT: D 275 ASN cc_start: 0.8469 (t0) cc_final: 0.8199 (t0) REVERT: D 304 PHE cc_start: 0.8561 (p90) cc_final: 0.8280 (p90) REVERT: D 344 PHE cc_start: 0.8407 (p90) cc_final: 0.7738 (p90) REVERT: D 362 ASN cc_start: 0.8355 (t0) cc_final: 0.7806 (t0) REVERT: D 364 SER cc_start: 0.8845 (m) cc_final: 0.8507 (p) REVERT: D 372 THR cc_start: 0.8678 (p) cc_final: 0.8238 (t) REVERT: D 373 MET cc_start: 0.8341 (mmm) cc_final: 0.7718 (mmm) REVERT: D 377 GLU cc_start: 0.8474 (tt0) cc_final: 0.7902 (tt0) REVERT: D 387 ASN cc_start: 0.8189 (t0) cc_final: 0.7382 (p0) REVERT: D 428 THR cc_start: 0.8669 (p) cc_final: 0.8408 (t) REVERT: D 458 ASN cc_start: 0.8197 (m-40) cc_final: 0.7969 (m-40) REVERT: D 466 VAL cc_start: 0.8691 (t) cc_final: 0.8441 (p) REVERT: D 474 ASN cc_start: 0.8290 (t0) cc_final: 0.8039 (t0) REVERT: D 511 GLN cc_start: 0.8735 (mt0) cc_final: 0.7777 (mt0) REVERT: D 514 VAL cc_start: 0.8732 (t) cc_final: 0.8433 (m) outliers start: 43 outliers final: 39 residues processed: 287 average time/residue: 0.2138 time to fit residues: 88.7546 Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 151 ARG 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 400 VAL 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 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 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 291 ARG Chi-restraints excluded: chain D residue 312 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 461 ILE 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 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 128 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 516 GLN D 95 HIS D 265 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.085648 restraints weight = 17071.800| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.50 r_work: 0.2879 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2991 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= 0.132 Angle : 0.534 11.510 14166 Z= 0.266 Chirality : 0.046 0.144 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.965 19.352 1422 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.86 % Allowed : 18.71 % Favored : 78.43 % 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: -0.62 (0.22), residues: 1320 helix: -0.15 (0.81), residues: 50 sheet: 0.33 (0.27), residues: 373 loop : -0.77 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 316 HIS 0.004 0.001 HIS D 277 PHE 0.021 0.001 PHE D 523 TYR 0.013 0.001 TYR B 369 ARG 0.003 0.000 ARG C 216 *********************** 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 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8914 (p-90) cc_final: 0.8199 (p-90) REVERT: A 123 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8506 (m) REVERT: A 206 THR cc_start: 0.8971 (m) cc_final: 0.8607 (t) REVERT: B 74 TYR cc_start: 0.8793 (t80) cc_final: 0.8285 (t80) REVERT: B 75 ASN cc_start: 0.8387 (t0) cc_final: 0.8121 (t0) REVERT: B 106 LEU cc_start: 0.8120 (mt) cc_final: 0.7767 (mt) REVERT: B 143 GLU cc_start: 0.8272 (pp20) cc_final: 0.7909 (pp20) REVERT: B 149 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 168 ILE cc_start: 0.8432 (tp) cc_final: 0.8184 (tt) REVERT: B 177 MET cc_start: 0.8691 (mmm) cc_final: 0.8412 (mmp) REVERT: B 219 GLU cc_start: 0.7714 (mp0) cc_final: 0.7309 (mp0) REVERT: B 257 TRP cc_start: 0.8884 (m100) cc_final: 0.8657 (m100) REVERT: B 295 ILE cc_start: 0.8263 (mt) cc_final: 0.7863 (mt) REVERT: B 298 ASP cc_start: 0.7766 (p0) cc_final: 0.7415 (p0) REVERT: B 338 ASP cc_start: 0.8316 (p0) cc_final: 0.7859 (p0) REVERT: B 339 MET cc_start: 0.8248 (mtp) cc_final: 0.7938 (mtp) REVERT: B 349 ILE cc_start: 0.8423 (mp) cc_final: 0.8202 (mm) REVERT: B 372 THR cc_start: 0.8497 (p) cc_final: 0.8078 (t) REVERT: B 373 MET cc_start: 0.8787 (mmp) cc_final: 0.8290 (mmp) REVERT: B 377 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 413 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8273 (mm-40) REVERT: B 444 VAL cc_start: 0.8934 (t) cc_final: 0.8622 (m) REVERT: B 468 ARG cc_start: 0.8354 (mtt180) cc_final: 0.8003 (mtt90) REVERT: B 481 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6643 (t0) REVERT: B 518 ASN cc_start: 0.8120 (m-40) cc_final: 0.7689 (t0) REVERT: B 530 VAL cc_start: 0.8924 (t) cc_final: 0.8701 (p) REVERT: B 546 ASP cc_start: 0.7964 (t70) cc_final: 0.7733 (t0) REVERT: B 548 SER cc_start: 0.8469 (m) cc_final: 0.8125 (p) REVERT: B 566 VAL cc_start: 0.8774 (t) cc_final: 0.8390 (p) REVERT: C 99 ASN cc_start: 0.8167 (m-40) cc_final: 0.7746 (m-40) REVERT: D 149 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 151 ARG cc_start: 0.8616 (ptt180) cc_final: 0.6820 (ttt180) REVERT: D 271 PHE cc_start: 0.8887 (p90) cc_final: 0.8475 (p90) REVERT: D 304 PHE cc_start: 0.8473 (p90) cc_final: 0.8199 (p90) REVERT: D 362 ASN cc_start: 0.8356 (t0) cc_final: 0.7864 (t0) REVERT: D 364 SER cc_start: 0.8842 (m) cc_final: 0.8495 (p) REVERT: D 372 THR cc_start: 0.8627 (p) cc_final: 0.8207 (t) REVERT: D 373 MET cc_start: 0.8318 (mmm) cc_final: 0.7918 (mmm) REVERT: D 377 GLU cc_start: 0.8486 (tt0) cc_final: 0.7773 (tt0) REVERT: D 380 PHE cc_start: 0.7928 (m-80) cc_final: 0.7628 (m-80) REVERT: D 387 ASN cc_start: 0.8105 (t0) cc_final: 0.7374 (p0) REVERT: D 428 THR cc_start: 0.8654 (p) cc_final: 0.8382 (t) REVERT: D 466 VAL cc_start: 0.8586 (t) cc_final: 0.8277 (p) REVERT: D 511 GLN cc_start: 0.8737 (mt0) cc_final: 0.7816 (mt0) outliers start: 31 outliers final: 25 residues processed: 279 average time/residue: 0.2059 time to fit residues: 82.4797 Evaluate side-chains 284 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 400 VAL 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 D residue 71 ASN 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 312 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 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.0040 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5814 ------------------------------------------------------------------------------- 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** D 94 GLN D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089298 restraints weight = 16670.478| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.33 r_work: 0.2887 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10319 Z= 0.172 Angle : 0.552 11.525 14166 Z= 0.273 Chirality : 0.047 0.166 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.945 19.036 1422 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.76 % Allowed : 18.71 % Favored : 78.53 % 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: -0.55 (0.22), residues: 1320 helix: 0.01 (0.82), residues: 50 sheet: 0.37 (0.27), residues: 384 loop : -0.73 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 316 HIS 0.004 0.001 HIS D 277 PHE 0.020 0.001 PHE D 523 TYR 0.013 0.001 TYR B 369 ARG 0.003 0.000 ARG C 216 ********************** 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 293 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8925 (p-90) cc_final: 0.8241 (p-90) REVERT: A 123 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8495 (m) REVERT: A 206 THR cc_start: 0.8988 (m) cc_final: 0.8509 (p) REVERT: B 74 TYR cc_start: 0.8808 (t80) cc_final: 0.8305 (t80) REVERT: B 75 ASN cc_start: 0.8407 (t0) cc_final: 0.8138 (t0) REVERT: B 143 GLU cc_start: 0.8218 (pp20) cc_final: 0.7908 (pp20) REVERT: B 149 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7055 (mm-30) REVERT: B 177 MET cc_start: 0.8698 (mmm) cc_final: 0.8436 (mmp) REVERT: B 219 GLU cc_start: 0.7664 (mp0) cc_final: 0.7290 (mp0) REVERT: B 257 TRP cc_start: 0.8905 (m100) cc_final: 0.8650 (m100) REVERT: B 295 ILE cc_start: 0.8287 (mt) cc_final: 0.7875 (mt) REVERT: B 298 ASP cc_start: 0.7759 (p0) cc_final: 0.7424 (p0) REVERT: B 338 ASP cc_start: 0.8275 (p0) cc_final: 0.7868 (p0) REVERT: B 349 ILE cc_start: 0.8366 (mp) cc_final: 0.8157 (mm) REVERT: B 372 THR cc_start: 0.8515 (p) cc_final: 0.8222 (t) REVERT: B 373 MET cc_start: 0.8753 (mmp) cc_final: 0.8275 (mmp) REVERT: B 377 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 444 VAL cc_start: 0.8910 (t) cc_final: 0.8608 (m) REVERT: B 481 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6720 (t0) REVERT: B 518 ASN cc_start: 0.8056 (m-40) cc_final: 0.7731 (t0) REVERT: B 530 VAL cc_start: 0.8939 (t) cc_final: 0.8718 (p) REVERT: B 546 ASP cc_start: 0.7928 (t70) cc_final: 0.7709 (t0) REVERT: B 548 SER cc_start: 0.8485 (m) cc_final: 0.8157 (p) REVERT: B 566 VAL cc_start: 0.8831 (t) cc_final: 0.8470 (p) REVERT: C 99 ASN cc_start: 0.8236 (m-40) cc_final: 0.7801 (m-40) REVERT: C 177 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7487 (mmp) REVERT: D 149 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7613 (mm-30) REVERT: D 151 ARG cc_start: 0.8620 (ptt180) cc_final: 0.6857 (ttt180) REVERT: D 213 VAL cc_start: 0.7991 (t) cc_final: 0.7671 (p) REVERT: D 271 PHE cc_start: 0.8789 (p90) cc_final: 0.8527 (p90) REVERT: D 362 ASN cc_start: 0.8335 (t0) cc_final: 0.7869 (t0) REVERT: D 364 SER cc_start: 0.8827 (m) cc_final: 0.8495 (p) REVERT: D 372 THR cc_start: 0.8629 (p) cc_final: 0.8220 (t) REVERT: D 373 MET cc_start: 0.8273 (mmm) cc_final: 0.7828 (mmm) REVERT: D 377 GLU cc_start: 0.8421 (tt0) cc_final: 0.7732 (tt0) REVERT: D 380 PHE cc_start: 0.7950 (m-80) cc_final: 0.7673 (m-80) REVERT: D 387 ASN cc_start: 0.8203 (t0) cc_final: 0.7485 (p0) REVERT: D 420 VAL cc_start: 0.8949 (t) cc_final: 0.8635 (m) REVERT: D 428 THR cc_start: 0.8681 (p) cc_final: 0.8409 (t) REVERT: D 466 VAL cc_start: 0.8598 (t) cc_final: 0.8274 (p) REVERT: D 511 GLN cc_start: 0.8711 (mt0) cc_final: 0.7861 (mt0) outliers start: 30 outliers final: 25 residues processed: 278 average time/residue: 0.2118 time to fit residues: 84.6207 Evaluate side-chains 291 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 400 VAL 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 177 MET 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 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 312 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 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 549 ASP 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: 0.3980 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.085967 restraints weight = 17028.203| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.46 r_work: 0.2867 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10319 Z= 0.221 Angle : 0.574 11.832 14166 Z= 0.284 Chirality : 0.047 0.158 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.040 18.962 1422 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.04 % Allowed : 18.53 % Favored : 78.43 % 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: -0.62 (0.22), residues: 1320 helix: -0.05 (0.81), residues: 50 sheet: 0.30 (0.27), residues: 378 loop : -0.77 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 316 HIS 0.004 0.001 HIS B 95 PHE 0.020 0.001 PHE D 523 TYR 0.013 0.001 TYR D 91 ARG 0.004 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.33 seconds wall clock time: 89 minutes 36.77 seconds (5376.77 seconds total)