Starting phenix.real_space_refine on Wed Sep 17 16:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jji_61528/09_2025/9jji_61528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jji_61528/09_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_61528/09_2025/9jji_61528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jji_61528/09_2025/9jji_61528.map" model { file = "/net/cci-nas-00/data/ceres_data/9jji_61528/09_2025/9jji_61528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jji_61528/09_2025/9jji_61528.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 399.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.84 Time building geometry restraints manager: 1.26 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10319 Z= 0.197 Angle : 0.601 4.830 14166 Z= 0.325 Chirality : 0.047 0.135 1582 Planarity : 0.004 0.038 1869 Dihedral : 12.411 89.356 3598 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B 291 TYR 0.029 0.002 TYR C 195 PHE 0.019 0.002 PHE B 357 TRP 0.019 0.001 TRP D 278 HIS 0.004 0.001 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00458 (10319) covalent geometry : angle 0.60130 (14166) hydrogen bonds : bond 0.25347 ( 292) hydrogen bonds : angle 9.95872 ( 741) *********************** 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 : 0.381 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: 0.7721 (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: 0.6885 (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: 0.7583 (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: 0.8630 (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: 0.7098 (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: 0.7821 (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: 0.8456 (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: 0.7339 (mmm) REVERT: D 377 GLU cc_start: 0.7951 (tt0) cc_final: 0.7343 (tt0) REVERT: D 389 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7170 (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: 0.7405 (mt0) REVERT: D 514 VAL cc_start: 0.8719 (t) cc_final: 0.8211 (p) REVERT: D 523 PHE cc_start: 0.8376 (p90) cc_final: 0.8009 (p90) REVERT: D 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7436 (m-30) REVERT: D 567 TYR cc_start: 0.7852 (t80) cc_final: 0.7431 (t80) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.0949 time to fit residues: 38.7855 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.099501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086349 restraints weight = 16812.111| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.34 r_work: 0.2855 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1511 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= 0.155 Angle : 0.579 7.425 14166 Z= 0.296 Chirality : 0.048 0.172 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.165 18.349 1422 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.66 % Allowed : 8.94 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.22), residues: 1320 helix: -1.00 (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 ARG 0.004 0.001 ARG D 299 TYR 0.013 0.002 TYR D 91 PHE 0.015 0.002 PHE B 78 TRP 0.013 0.001 TRP D 68 HIS 0.006 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00359 (10319) covalent geometry : angle 0.57896 (14166) hydrogen bonds : bond 0.04362 ( 292) hydrogen bonds : angle 7.12051 ( 741) *********************** 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 277 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.361 Fit side-chains REVERT: A 113 TRP cc_start: 0.8969 (p-90) cc_final: 0.8292 (p-90) REVERT: A 128 VAL cc_start: 0.8499 (m) cc_final: 0.8219 (t) REVERT: A 206 THR cc_start: 0.8898 (m) cc_final: 0.8315 (p) REVERT: B 74 TYR cc_start: 0.8805 (t80) cc_final: 0.8225 (t80) REVERT: B 143 GLU cc_start: 0.8264 (pp20) cc_final: 0.7926 (pp20) REVERT: B 151 ARG cc_start: 0.5792 (ptm160) cc_final: 0.5350 (ptm160) REVERT: B 172 ASP cc_start: 0.7954 (t70) cc_final: 0.7245 (t70) REVERT: B 262 VAL cc_start: 0.9031 (m) cc_final: 0.8647 (t) REVERT: B 295 ILE cc_start: 0.8211 (mt) cc_final: 0.7890 (mt) REVERT: B 298 ASP cc_start: 0.7425 (p0) cc_final: 0.7010 (p0) REVERT: B 369 TYR cc_start: 0.8016 (m-10) cc_final: 0.7737 (m-10) REVERT: B 373 MET cc_start: 0.8793 (mmp) cc_final: 0.8349 (mmp) REVERT: B 398 GLN cc_start: 0.8354 (mt0) cc_final: 0.8049 (mt0) REVERT: B 413 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8372 (mm-40) REVERT: B 444 VAL cc_start: 0.8703 (t) cc_final: 0.8328 (m) REVERT: B 455 ILE cc_start: 0.8454 (tp) cc_final: 0.8149 (pt) REVERT: B 530 VAL cc_start: 0.8834 (t) cc_final: 0.8609 (p) REVERT: B 546 ASP cc_start: 0.7916 (t70) cc_final: 0.7597 (t0) REVERT: B 548 SER cc_start: 0.8651 (m) cc_final: 0.8330 (p) REVERT: B 566 VAL cc_start: 0.8828 (t) cc_final: 0.8607 (m) REVERT: C 99 ASN cc_start: 0.8071 (m-40) cc_final: 0.7776 (m110) REVERT: D 151 ARG cc_start: 0.8645 (ptt180) cc_final: 0.6945 (ttt180) REVERT: D 152 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7530 (mm-40) REVERT: D 210 GLN cc_start: 0.8379 (mm110) cc_final: 0.8079 (mm110) REVERT: D 213 VAL cc_start: 0.7902 (t) cc_final: 0.7701 (m) REVERT: D 271 PHE cc_start: 0.8885 (p90) cc_final: 0.8481 (p90) REVERT: D 344 PHE cc_start: 0.8368 (p90) cc_final: 0.8104 (p90) REVERT: D 362 ASN cc_start: 0.8232 (t0) cc_final: 0.7749 (t0) REVERT: D 364 SER cc_start: 0.8841 (m) cc_final: 0.8493 (p) REVERT: D 373 MET cc_start: 0.8191 (mmm) cc_final: 0.7734 (mmm) REVERT: D 377 GLU cc_start: 0.8457 (tt0) cc_final: 0.7849 (tt0) REVERT: D 387 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.6974 (p0) REVERT: D 428 THR cc_start: 0.8557 (p) cc_final: 0.8241 (t) REVERT: D 466 VAL cc_start: 0.8674 (t) cc_final: 0.8333 (p) REVERT: D 511 GLN cc_start: 0.8734 (mt0) cc_final: 0.8459 (mt0) REVERT: D 514 VAL cc_start: 0.8646 (t) cc_final: 0.8411 (m) REVERT: D 523 PHE cc_start: 0.8263 (p90) cc_final: 0.7959 (p90) REVERT: D 549 ASP cc_start: 0.8072 (m-30) cc_final: 0.7850 (m-30) REVERT: D 566 VAL cc_start: 0.8476 (t) cc_final: 0.8213 (t) outliers start: 18 outliers final: 15 residues processed: 265 average time/residue: 0.0984 time to fit residues: 37.0789 Evaluate side-chains 257 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 495 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 104 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.094296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.081032 restraints weight = 17448.741| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.52 r_work: 0.2794 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10319 Z= 0.234 Angle : 0.602 6.861 14166 Z= 0.310 Chirality : 0.049 0.195 1582 Planarity : 0.005 0.042 1869 Dihedral : 4.367 18.332 1422 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.86 % Allowed : 11.43 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1320 helix: -1.15 (0.76), residues: 50 sheet: 0.20 (0.25), residues: 406 loop : -0.79 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 174 TYR 0.016 0.002 TYR D 91 PHE 0.019 0.002 PHE D 223 TRP 0.017 0.002 TRP D 68 HIS 0.006 0.002 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00548 (10319) covalent geometry : angle 0.60180 (14166) hydrogen bonds : bond 0.04903 ( 292) hydrogen bonds : angle 6.78341 ( 741) *********************** 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 289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 128 VAL cc_start: 0.8407 (m) cc_final: 0.8166 (t) REVERT: A 206 THR cc_start: 0.8945 (m) cc_final: 0.8500 (t) REVERT: B 74 TYR cc_start: 0.8854 (t80) cc_final: 0.8302 (t80) REVERT: B 75 ASN cc_start: 0.8561 (t0) cc_final: 0.8130 (t0) REVERT: B 143 GLU cc_start: 0.8264 (pp20) cc_final: 0.7927 (pp20) REVERT: B 262 VAL cc_start: 0.9020 (m) cc_final: 0.8748 (t) REVERT: B 295 ILE cc_start: 0.8265 (mt) cc_final: 0.7923 (mt) REVERT: B 298 ASP cc_start: 0.7636 (p0) cc_final: 0.7198 (p0) REVERT: B 372 THR cc_start: 0.8571 (p) cc_final: 0.8076 (t) REVERT: B 398 GLN cc_start: 0.8408 (mt0) cc_final: 0.8087 (mt0) REVERT: B 413 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8365 (mm-40) REVERT: B 444 VAL cc_start: 0.8840 (t) cc_final: 0.8488 (m) REVERT: B 468 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8019 (mtt90) REVERT: B 518 ASN cc_start: 0.8278 (m-40) cc_final: 0.7908 (t0) REVERT: B 530 VAL cc_start: 0.8947 (t) cc_final: 0.8727 (p) REVERT: B 546 ASP cc_start: 0.7921 (t70) cc_final: 0.7623 (t0) REVERT: B 548 SER cc_start: 0.8704 (m) cc_final: 0.8324 (p) REVERT: B 559 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7787 (tpp80) REVERT: B 566 VAL cc_start: 0.8877 (t) cc_final: 0.8639 (m) REVERT: D 151 ARG cc_start: 0.8690 (ptt180) cc_final: 0.6937 (ttt180) REVERT: D 177 MET cc_start: 0.8039 (mmm) cc_final: 0.7750 (mmm) REVERT: D 210 GLN cc_start: 0.8394 (mm110) cc_final: 0.8064 (mm110) REVERT: D 271 PHE cc_start: 0.8891 (p90) cc_final: 0.8575 (p90) REVERT: D 275 ASN cc_start: 0.8491 (t0) cc_final: 0.8289 (t0) REVERT: D 344 PHE cc_start: 0.8383 (p90) cc_final: 0.8033 (p90) REVERT: D 362 ASN cc_start: 0.8369 (t0) cc_final: 0.7808 (t0) REVERT: D 364 SER cc_start: 0.8859 (m) cc_final: 0.8544 (p) REVERT: D 371 THR cc_start: 0.8306 (p) cc_final: 0.7608 (t) REVERT: D 373 MET cc_start: 0.8313 (mmm) cc_final: 0.7813 (mmm) REVERT: D 377 GLU cc_start: 0.8509 (tt0) cc_final: 0.7824 (tt0) REVERT: D 387 ASN cc_start: 0.8093 (t0) cc_final: 0.7229 (p0) REVERT: D 389 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7647 (mm-40) REVERT: D 419 PHE cc_start: 0.8723 (t80) cc_final: 0.8427 (t80) REVERT: D 420 VAL cc_start: 0.8779 (t) cc_final: 0.8468 (m) REVERT: D 428 THR cc_start: 0.8617 (p) cc_final: 0.8366 (t) REVERT: D 466 VAL cc_start: 0.8682 (t) cc_final: 0.8402 (p) REVERT: D 511 GLN cc_start: 0.8759 (mt0) cc_final: 0.7810 (mt0) REVERT: D 514 VAL cc_start: 0.8700 (t) cc_final: 0.8390 (m) REVERT: D 523 PHE cc_start: 0.8259 (p90) cc_final: 0.7986 (p90) REVERT: D 566 VAL cc_start: 0.8523 (t) cc_final: 0.7919 (m) outliers start: 31 outliers final: 26 residues processed: 273 average time/residue: 0.0882 time to fit residues: 34.6988 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 : 0.360 ------------------------------------------------------------------------------- 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 227 ARG 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 187 VAL Chi-restraints excluded: chain D residue 237 ILE 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 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.081486 restraints weight = 17424.425| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.55 r_work: 0.2826 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10319 Z= 0.197 Angle : 0.575 7.510 14166 Z= 0.295 Chirality : 0.048 0.143 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.321 18.177 1422 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.59 % Allowed : 13.09 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.21), residues: 1320 helix: -1.06 (0.76), residues: 50 sheet: 0.27 (0.26), residues: 392 loop : -0.91 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 276 TYR 0.015 0.002 TYR D 91 PHE 0.015 0.002 PHE D 223 TRP 0.018 0.002 TRP D 68 HIS 0.005 0.002 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00462 (10319) covalent geometry : angle 0.57531 (14166) hydrogen bonds : bond 0.04313 ( 292) hydrogen bonds : angle 6.60210 ( 741) *********************** 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 308 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 206 THR cc_start: 0.8993 (m) cc_final: 0.8624 (t) REVERT: B 74 TYR cc_start: 0.8872 (t80) cc_final: 0.8374 (t80) REVERT: B 75 ASN cc_start: 0.8525 (t0) cc_final: 0.8179 (t0) REVERT: B 143 GLU cc_start: 0.8275 (pp20) cc_final: 0.7975 (pp20) REVERT: B 149 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7174 (mm-30) REVERT: B 219 GLU cc_start: 0.7772 (mp0) cc_final: 0.7386 (mp0) REVERT: B 295 ILE cc_start: 0.8285 (mt) cc_final: 0.7942 (mt) REVERT: B 298 ASP cc_start: 0.7694 (p0) cc_final: 0.7303 (p0) REVERT: B 339 MET cc_start: 0.8470 (mtp) cc_final: 0.8163 (mtp) REVERT: B 349 ILE cc_start: 0.8421 (mp) cc_final: 0.8197 (mm) REVERT: B 369 TYR cc_start: 0.8150 (m-10) cc_final: 0.7838 (m-10) REVERT: B 372 THR cc_start: 0.8576 (p) cc_final: 0.8126 (t) REVERT: B 373 MET cc_start: 0.8850 (mmp) cc_final: 0.8344 (mmp) REVERT: B 377 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 413 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8407 (mm-40) REVERT: B 444 VAL cc_start: 0.8869 (t) cc_final: 0.8532 (m) REVERT: B 530 VAL cc_start: 0.8871 (t) cc_final: 0.8660 (p) REVERT: B 546 ASP cc_start: 0.7944 (t70) cc_final: 0.7694 (t0) REVERT: B 548 SER cc_start: 0.8675 (m) cc_final: 0.8309 (p) REVERT: B 566 VAL cc_start: 0.8898 (t) cc_final: 0.8585 (m) REVERT: D 82 VAL cc_start: 0.8966 (p) cc_final: 0.8605 (t) REVERT: D 149 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7842 (mm-30) REVERT: D 151 ARG cc_start: 0.8735 (ptt180) cc_final: 0.7127 (ptm160) REVERT: D 271 PHE cc_start: 0.8914 (p90) cc_final: 0.8561 (p90) REVERT: D 275 ASN cc_start: 0.8508 (t0) cc_final: 0.8279 (t0) REVERT: D 304 PHE cc_start: 0.8513 (p90) cc_final: 0.8205 (p90) REVERT: D 316 TRP cc_start: 0.8527 (t60) cc_final: 0.8255 (t60) REVERT: D 344 PHE cc_start: 0.8407 (p90) cc_final: 0.7873 (p90) REVERT: D 362 ASN cc_start: 0.8386 (t0) cc_final: 0.7848 (t0) REVERT: D 364 SER cc_start: 0.8856 (m) cc_final: 0.8541 (p) REVERT: D 371 THR cc_start: 0.8369 (p) cc_final: 0.7695 (t) REVERT: D 373 MET cc_start: 0.8270 (mmm) cc_final: 0.7805 (mmm) REVERT: D 377 GLU cc_start: 0.8490 (tt0) cc_final: 0.7807 (tt0) REVERT: D 387 ASN cc_start: 0.8151 (t0) cc_final: 0.7183 (p0) REVERT: D 389 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7634 (mm-40) REVERT: D 420 VAL cc_start: 0.8878 (t) cc_final: 0.8537 (m) REVERT: D 428 THR cc_start: 0.8669 (p) cc_final: 0.8411 (t) REVERT: D 466 VAL cc_start: 0.8648 (t) cc_final: 0.8354 (p) REVERT: D 511 GLN cc_start: 0.8772 (mt0) cc_final: 0.7779 (mt0) REVERT: D 514 VAL cc_start: 0.8702 (t) cc_final: 0.8397 (m) REVERT: D 566 VAL cc_start: 0.8547 (t) cc_final: 0.8057 (m) outliers start: 39 outliers final: 33 residues processed: 284 average time/residue: 0.0851 time to fit residues: 34.8038 Evaluate side-chains 289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 531 ASP 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 189 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 206 THR 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 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN C 99 ASN D 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085259 restraints weight = 16824.001| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.29 r_work: 0.2829 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10319 Z= 0.312 Angle : 0.648 8.632 14166 Z= 0.338 Chirality : 0.051 0.177 1582 Planarity : 0.006 0.047 1869 Dihedral : 4.757 21.480 1422 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.15 % Allowed : 14.75 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1320 helix: -1.24 (0.73), residues: 50 sheet: 0.07 (0.25), residues: 407 loop : -1.03 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 151 TYR 0.022 0.002 TYR D 91 PHE 0.021 0.002 PHE D 523 TRP 0.023 0.002 TRP D 68 HIS 0.007 0.002 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00725 (10319) covalent geometry : angle 0.64827 (14166) hydrogen bonds : bond 0.05231 ( 292) hydrogen bonds : angle 6.76889 ( 741) *********************** 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 319 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 0.324 Fit side-chains REVERT: A 206 THR cc_start: 0.9037 (m) cc_final: 0.8677 (t) REVERT: B 74 TYR cc_start: 0.8844 (t80) cc_final: 0.8518 (t80) REVERT: B 75 ASN cc_start: 0.8537 (t0) cc_final: 0.8226 (t0) REVERT: B 143 GLU cc_start: 0.8230 (pp20) cc_final: 0.7898 (pp20) REVERT: B 149 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 177 MET cc_start: 0.8724 (mmm) cc_final: 0.8373 (mmp) REVERT: B 219 GLU cc_start: 0.7738 (mp0) cc_final: 0.7260 (mp0) REVERT: B 260 GLU cc_start: 0.8003 (tt0) cc_final: 0.7774 (tt0) REVERT: B 295 ILE cc_start: 0.8326 (mt) cc_final: 0.7942 (mt) REVERT: B 349 ILE cc_start: 0.8426 (mp) cc_final: 0.8205 (mm) REVERT: B 372 THR cc_start: 0.8560 (p) cc_final: 0.8083 (t) REVERT: B 377 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 413 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8370 (mm-40) REVERT: B 444 VAL cc_start: 0.8921 (t) cc_final: 0.8602 (m) REVERT: B 481 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6502 (t0) REVERT: B 518 ASN cc_start: 0.8246 (m-40) cc_final: 0.7853 (t0) REVERT: B 543 THR cc_start: 0.8586 (m) cc_final: 0.8338 (p) REVERT: B 546 ASP cc_start: 0.8029 (t70) cc_final: 0.7769 (t0) REVERT: B 548 SER cc_start: 0.8615 (m) cc_final: 0.8274 (p) REVERT: B 566 VAL cc_start: 0.8974 (t) cc_final: 0.8629 (p) REVERT: D 82 VAL cc_start: 0.8937 (p) cc_final: 0.8560 (t) REVERT: D 149 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 151 ARG cc_start: 0.8779 (ptt180) cc_final: 0.7253 (ptm160) REVERT: D 257 TRP cc_start: 0.8824 (m100) cc_final: 0.7974 (m100) REVERT: D 271 PHE cc_start: 0.8889 (p90) cc_final: 0.8507 (p90) REVERT: D 275 ASN cc_start: 0.8404 (t0) cc_final: 0.8172 (t0) REVERT: D 316 TRP cc_start: 0.8692 (t60) cc_final: 0.8428 (t60) REVERT: D 344 PHE cc_start: 0.8382 (p90) cc_final: 0.7736 (p90) REVERT: D 362 ASN cc_start: 0.8352 (t0) cc_final: 0.7852 (t0) REVERT: D 364 SER cc_start: 0.8839 (m) cc_final: 0.8524 (p) REVERT: D 371 THR cc_start: 0.8476 (p) cc_final: 0.7838 (t) REVERT: D 373 MET cc_start: 0.8248 (mmm) cc_final: 0.7829 (mmm) REVERT: D 377 GLU cc_start: 0.8383 (tt0) cc_final: 0.7715 (tt0) REVERT: D 387 ASN cc_start: 0.8233 (t0) cc_final: 0.7208 (p0) REVERT: D 389 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7634 (mm-40) REVERT: D 420 VAL cc_start: 0.8953 (t) cc_final: 0.8534 (m) REVERT: D 428 THR cc_start: 0.8731 (p) cc_final: 0.8487 (t) REVERT: D 466 VAL cc_start: 0.8686 (t) cc_final: 0.8465 (p) REVERT: D 511 GLN cc_start: 0.8722 (mt0) cc_final: 0.7772 (mt0) REVERT: D 514 VAL cc_start: 0.8737 (t) cc_final: 0.8445 (m) outliers start: 45 outliers final: 39 residues processed: 296 average time/residue: 0.0863 time to fit residues: 36.8422 Evaluate side-chains 304 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 215 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 400 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 79 THR 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 189 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 83 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN C 99 ASN D 265 GLN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.082315 restraints weight = 17519.218| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.53 r_work: 0.2816 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10319 Z= 0.184 Angle : 0.586 9.983 14166 Z= 0.298 Chirality : 0.048 0.166 1582 Planarity : 0.005 0.044 1869 Dihedral : 4.456 20.197 1422 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.06 % Allowed : 16.50 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.21), residues: 1320 helix: -0.80 (0.77), residues: 50 sheet: 0.01 (0.26), residues: 398 loop : -1.03 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 559 TYR 0.017 0.002 TYR D 91 PHE 0.013 0.001 PHE B 78 TRP 0.015 0.002 TRP D 68 HIS 0.005 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00432 (10319) covalent geometry : angle 0.58563 (14166) hydrogen bonds : bond 0.04242 ( 292) hydrogen bonds : angle 6.52448 ( 741) *********************** 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 316 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.371 Fit side-chains REVERT: A 123 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8434 (m) REVERT: A 151 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8025 (mtm110) REVERT: A 206 THR cc_start: 0.8988 (m) cc_final: 0.8663 (t) REVERT: A 227 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.8402 (ptt-90) REVERT: B 74 TYR cc_start: 0.8881 (t80) cc_final: 0.8451 (t80) REVERT: B 75 ASN cc_start: 0.8516 (t0) cc_final: 0.8213 (t0) REVERT: B 143 GLU cc_start: 0.8256 (pp20) cc_final: 0.7885 (pp20) REVERT: B 149 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 177 MET cc_start: 0.8693 (mmm) cc_final: 0.8325 (mmp) REVERT: B 219 GLU cc_start: 0.7768 (mp0) cc_final: 0.7292 (mp0) REVERT: B 260 GLU cc_start: 0.8020 (tt0) cc_final: 0.7809 (tt0) REVERT: B 295 ILE cc_start: 0.8280 (mt) cc_final: 0.7918 (mt) REVERT: B 338 ASP cc_start: 0.8337 (p0) cc_final: 0.7953 (p0) REVERT: B 349 ILE cc_start: 0.8433 (mp) cc_final: 0.8221 (mm) REVERT: B 372 THR cc_start: 0.8536 (p) cc_final: 0.8147 (t) REVERT: B 377 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 413 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8343 (mm-40) REVERT: B 444 VAL cc_start: 0.8953 (t) cc_final: 0.8668 (m) REVERT: B 481 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6514 (t0) REVERT: B 507 LEU cc_start: 0.8741 (tp) cc_final: 0.8441 (mp) REVERT: B 546 ASP cc_start: 0.8046 (t70) cc_final: 0.7774 (t0) REVERT: B 548 SER cc_start: 0.8530 (m) cc_final: 0.8191 (p) REVERT: B 566 VAL cc_start: 0.8877 (t) cc_final: 0.8498 (p) REVERT: D 108 GLN cc_start: 0.8857 (tt0) cc_final: 0.8567 (tt0) REVERT: D 149 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 151 ARG cc_start: 0.8725 (ptt180) cc_final: 0.7142 (ptm160) REVERT: D 257 TRP cc_start: 0.8677 (m100) cc_final: 0.8040 (m100) REVERT: D 271 PHE cc_start: 0.8907 (p90) cc_final: 0.8530 (p90) REVERT: D 275 ASN cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: D 316 TRP cc_start: 0.8623 (t60) cc_final: 0.8269 (t60) REVERT: D 344 PHE cc_start: 0.8378 (p90) cc_final: 0.7660 (p90) REVERT: D 362 ASN cc_start: 0.8394 (t0) cc_final: 0.7875 (t0) REVERT: D 364 SER cc_start: 0.8855 (m) cc_final: 0.8523 (p) REVERT: D 371 THR cc_start: 0.8522 (p) cc_final: 0.7838 (t) REVERT: D 373 MET cc_start: 0.8359 (mmm) cc_final: 0.7920 (mmm) REVERT: D 377 GLU cc_start: 0.8433 (tt0) cc_final: 0.7727 (tt0) REVERT: D 387 ASN cc_start: 0.8218 (t0) cc_final: 0.7224 (p0) REVERT: D 389 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7673 (mm-40) REVERT: D 420 VAL cc_start: 0.8916 (t) cc_final: 0.8470 (m) REVERT: D 428 THR cc_start: 0.8704 (p) cc_final: 0.8441 (t) REVERT: D 466 VAL cc_start: 0.8676 (t) cc_final: 0.8440 (p) REVERT: D 511 GLN cc_start: 0.8743 (mt0) cc_final: 0.7752 (mt0) REVERT: D 514 VAL cc_start: 0.8724 (t) cc_final: 0.8405 (m) outliers start: 44 outliers final: 32 residues processed: 292 average time/residue: 0.0889 time to fit residues: 37.4402 Evaluate side-chains 301 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 163 LEU 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 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 187 VAL Chi-restraints excluded: chain C residue 189 THR 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 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 330 GLN Chi-restraints excluded: chain D residue 372 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 545 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 0.0570 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 516 GLN D 94 GLN D 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.084271 restraints weight = 17231.968| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.54 r_work: 0.2837 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10319 Z= 0.099 Angle : 0.538 10.478 14166 Z= 0.268 Chirality : 0.046 0.159 1582 Planarity : 0.005 0.043 1869 Dihedral : 4.067 19.394 1422 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.32 % Allowed : 17.60 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.21), residues: 1320 helix: -0.34 (0.82), residues: 50 sheet: 0.12 (0.26), residues: 379 loop : -0.90 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.014 0.001 TYR B 369 PHE 0.011 0.001 PHE A 78 TRP 0.018 0.001 TRP D 68 HIS 0.004 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00231 (10319) covalent geometry : angle 0.53814 (14166) hydrogen bonds : bond 0.03237 ( 292) hydrogen bonds : angle 6.18605 ( 741) *********************** 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 310 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8928 (p-90) cc_final: 0.8162 (p-90) REVERT: A 123 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 151 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8060 (mtm110) REVERT: A 206 THR cc_start: 0.9005 (m) cc_final: 0.8622 (t) REVERT: A 227 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8426 (ptt-90) REVERT: B 74 TYR cc_start: 0.8793 (t80) cc_final: 0.8318 (t80) REVERT: B 75 ASN cc_start: 0.8395 (t0) cc_final: 0.8132 (t0) REVERT: B 143 GLU cc_start: 0.8279 (pp20) cc_final: 0.7906 (pp20) REVERT: B 149 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 151 ARG cc_start: 0.5054 (ptm160) cc_final: 0.4843 (ptm160) REVERT: B 168 ILE cc_start: 0.8418 (tp) cc_final: 0.8150 (tt) REVERT: B 177 MET cc_start: 0.8621 (mmm) cc_final: 0.8299 (mmp) REVERT: B 219 GLU cc_start: 0.7738 (mp0) cc_final: 0.7260 (mp0) REVERT: B 249 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (t) REVERT: B 295 ILE cc_start: 0.8300 (mt) cc_final: 0.7906 (mt) REVERT: B 338 ASP cc_start: 0.8219 (p0) cc_final: 0.7836 (p0) REVERT: B 339 MET cc_start: 0.8424 (mtp) cc_final: 0.8142 (mtp) REVERT: B 349 ILE cc_start: 0.8416 (mp) cc_final: 0.8215 (mm) REVERT: B 357 PHE cc_start: 0.8321 (m-80) cc_final: 0.8104 (m-80) REVERT: B 372 THR cc_start: 0.8487 (p) cc_final: 0.8150 (t) REVERT: B 373 MET cc_start: 0.8817 (mmp) cc_final: 0.8325 (mmp) REVERT: B 377 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 444 VAL cc_start: 0.8949 (t) cc_final: 0.8664 (m) REVERT: B 481 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6728 (t0) REVERT: B 507 LEU cc_start: 0.8689 (tp) cc_final: 0.8397 (mp) REVERT: B 518 ASN cc_start: 0.8142 (m-40) cc_final: 0.7661 (t0) REVERT: B 546 ASP cc_start: 0.8002 (t70) cc_final: 0.7743 (t0) REVERT: B 548 SER cc_start: 0.8526 (m) cc_final: 0.8192 (p) REVERT: B 566 VAL cc_start: 0.8778 (t) cc_final: 0.8385 (p) REVERT: D 108 GLN cc_start: 0.8788 (tt0) cc_final: 0.8472 (tt0) REVERT: D 149 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7637 (mm-30) REVERT: D 151 ARG cc_start: 0.8692 (ptt180) cc_final: 0.6788 (ttt180) REVERT: D 271 PHE cc_start: 0.8922 (p90) cc_final: 0.8554 (p90) REVERT: D 275 ASN cc_start: 0.8556 (t0) cc_final: 0.8354 (t0) REVERT: D 312 VAL cc_start: 0.8119 (m) cc_final: 0.7893 (t) REVERT: D 362 ASN cc_start: 0.8325 (t0) cc_final: 0.7855 (t0) REVERT: D 364 SER cc_start: 0.8856 (m) cc_final: 0.8510 (p) REVERT: D 371 THR cc_start: 0.8404 (p) cc_final: 0.7661 (t) REVERT: D 373 MET cc_start: 0.8396 (mmm) cc_final: 0.7832 (mmm) REVERT: D 387 ASN cc_start: 0.8178 (t0) cc_final: 0.7086 (p0) REVERT: D 389 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7621 (mm-40) REVERT: D 419 PHE cc_start: 0.8623 (t80) cc_final: 0.8396 (t80) REVERT: D 420 VAL cc_start: 0.8709 (t) cc_final: 0.8337 (m) REVERT: D 428 THR cc_start: 0.8667 (p) cc_final: 0.8410 (t) REVERT: D 466 VAL cc_start: 0.8638 (t) cc_final: 0.8363 (p) REVERT: D 511 GLN cc_start: 0.8748 (mt0) cc_final: 0.7782 (mt0) REVERT: D 568 ASN cc_start: 0.7887 (t0) cc_final: 0.7686 (t0) outliers start: 36 outliers final: 23 residues processed: 290 average time/residue: 0.0908 time to fit residues: 37.8017 Evaluate side-chains 294 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 THR 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 187 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 473 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 0.0870 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 0.0770 chunk 24 optimal weight: 0.0970 chunk 116 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 94 GLN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.086129 restraints weight = 17231.903| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.54 r_work: 0.2875 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3132 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= 0.086 Angle : 0.527 10.898 14166 Z= 0.258 Chirality : 0.046 0.200 1582 Planarity : 0.005 0.042 1869 Dihedral : 3.782 17.766 1422 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.76 % Allowed : 18.62 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.22), residues: 1320 helix: 0.01 (0.84), residues: 50 sheet: 0.27 (0.26), residues: 389 loop : -0.73 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.015 0.001 TYR B 369 PHE 0.013 0.001 PHE B 419 TRP 0.026 0.001 TRP D 316 HIS 0.004 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00198 (10319) covalent geometry : angle 0.52691 (14166) hydrogen bonds : bond 0.02797 ( 292) hydrogen bonds : angle 5.93421 ( 741) *********************** 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: 30 poor density : 280 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8902 (p-90) cc_final: 0.8137 (p-90) REVERT: A 123 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8523 (m) REVERT: A 206 THR cc_start: 0.8956 (m) cc_final: 0.8477 (p) REVERT: B 74 TYR cc_start: 0.8777 (t80) cc_final: 0.8301 (t80) REVERT: B 75 ASN cc_start: 0.8293 (t0) cc_final: 0.8085 (t0) REVERT: B 106 LEU cc_start: 0.8072 (mt) cc_final: 0.7764 (mt) REVERT: B 143 GLU cc_start: 0.8297 (pp20) cc_final: 0.7932 (pp20) REVERT: B 149 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 168 ILE cc_start: 0.8357 (tp) cc_final: 0.8130 (tt) REVERT: B 219 GLU cc_start: 0.7695 (mp0) cc_final: 0.7258 (mp0) REVERT: B 249 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7860 (t) REVERT: B 295 ILE cc_start: 0.8243 (mt) cc_final: 0.7871 (mt) REVERT: B 328 ILE cc_start: 0.9124 (tt) cc_final: 0.8884 (pt) REVERT: B 338 ASP cc_start: 0.8189 (p0) cc_final: 0.7793 (p0) REVERT: B 339 MET cc_start: 0.8340 (mtp) cc_final: 0.8082 (mtp) REVERT: B 349 ILE cc_start: 0.8400 (mp) cc_final: 0.8186 (mm) REVERT: B 357 PHE cc_start: 0.8257 (m-80) cc_final: 0.8034 (m-80) REVERT: B 372 THR cc_start: 0.8449 (p) cc_final: 0.8074 (t) REVERT: B 373 MET cc_start: 0.8724 (mmp) cc_final: 0.8297 (mmp) REVERT: B 377 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 444 VAL cc_start: 0.8954 (t) cc_final: 0.8658 (m) REVERT: B 481 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6785 (t0) REVERT: B 518 ASN cc_start: 0.7950 (m-40) cc_final: 0.7657 (t0) REVERT: B 546 ASP cc_start: 0.7892 (t70) cc_final: 0.7654 (t0) REVERT: B 548 SER cc_start: 0.8508 (m) cc_final: 0.8176 (p) REVERT: B 566 VAL cc_start: 0.8743 (t) cc_final: 0.8349 (p) REVERT: C 72 PHE cc_start: 0.8298 (m-80) cc_final: 0.8069 (m-80) REVERT: D 108 GLN cc_start: 0.8774 (tt0) cc_final: 0.8444 (tt0) REVERT: D 149 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7709 (mm-30) REVERT: D 151 ARG cc_start: 0.8703 (ptt180) cc_final: 0.6803 (ttt180) REVERT: D 271 PHE cc_start: 0.8914 (p90) cc_final: 0.8428 (p90) REVERT: D 304 PHE cc_start: 0.8405 (p90) cc_final: 0.8054 (p90) REVERT: D 362 ASN cc_start: 0.8346 (t0) cc_final: 0.7826 (t0) REVERT: D 364 SER cc_start: 0.8864 (m) cc_final: 0.8519 (p) REVERT: D 373 MET cc_start: 0.8416 (mmm) cc_final: 0.7896 (mmm) REVERT: D 387 ASN cc_start: 0.8167 (t0) cc_final: 0.6966 (p0) REVERT: D 389 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7601 (mm-40) REVERT: D 419 PHE cc_start: 0.8541 (t80) cc_final: 0.8269 (t80) REVERT: D 420 VAL cc_start: 0.8754 (t) cc_final: 0.8372 (m) REVERT: D 421 MET cc_start: 0.8475 (mmt) cc_final: 0.8111 (mmm) REVERT: D 428 THR cc_start: 0.8610 (p) cc_final: 0.8362 (t) REVERT: D 461 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8507 (pt) REVERT: D 511 GLN cc_start: 0.8756 (mt0) cc_final: 0.7853 (mt0) outliers start: 30 outliers final: 21 residues processed: 293 average time/residue: 0.0870 time to fit residues: 37.0445 Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 249 THR 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 189 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 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 330 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.095090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.082163 restraints weight = 17329.978| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.53 r_work: 0.2838 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10319 Z= 0.249 Angle : 0.636 11.700 14166 Z= 0.322 Chirality : 0.050 0.172 1582 Planarity : 0.006 0.045 1869 Dihedral : 4.310 19.193 1422 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.13 % Allowed : 19.08 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1320 helix: -0.26 (0.81), residues: 50 sheet: 0.09 (0.26), residues: 413 loop : -0.80 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 227 TYR 0.017 0.002 TYR D 91 PHE 0.017 0.002 PHE C 102 TRP 0.042 0.002 TRP D 316 HIS 0.007 0.002 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00584 (10319) covalent geometry : angle 0.63588 (14166) hydrogen bonds : bond 0.04581 ( 292) hydrogen bonds : angle 6.30399 ( 741) *********************** 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 308 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.350 Fit side-chains REVERT: A 123 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8447 (m) REVERT: A 206 THR cc_start: 0.8954 (m) cc_final: 0.8492 (p) REVERT: B 74 TYR cc_start: 0.8872 (t80) cc_final: 0.8415 (t80) REVERT: B 75 ASN cc_start: 0.8503 (t0) cc_final: 0.8179 (t0) REVERT: B 143 GLU cc_start: 0.8273 (pp20) cc_final: 0.7933 (pp20) REVERT: B 149 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 219 GLU cc_start: 0.7764 (mp0) cc_final: 0.7291 (mp0) REVERT: B 249 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7908 (t) REVERT: B 295 ILE cc_start: 0.8390 (mt) cc_final: 0.7984 (mt) REVERT: B 338 ASP cc_start: 0.8181 (p0) cc_final: 0.7825 (p0) REVERT: B 339 MET cc_start: 0.8460 (mtp) cc_final: 0.8215 (mtm) REVERT: B 349 ILE cc_start: 0.8370 (mp) cc_final: 0.8155 (mm) REVERT: B 357 PHE cc_start: 0.8265 (m-80) cc_final: 0.8063 (m-80) REVERT: B 372 THR cc_start: 0.8507 (p) cc_final: 0.8122 (t) REVERT: B 377 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 444 VAL cc_start: 0.8956 (t) cc_final: 0.8675 (m) REVERT: B 481 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6724 (t0) REVERT: B 507 LEU cc_start: 0.8789 (tp) cc_final: 0.8549 (mp) REVERT: B 518 ASN cc_start: 0.8154 (m-40) cc_final: 0.7656 (t0) REVERT: B 546 ASP cc_start: 0.8083 (t70) cc_final: 0.7830 (t0) REVERT: B 548 SER cc_start: 0.8510 (m) cc_final: 0.8207 (p) REVERT: B 566 VAL cc_start: 0.8893 (t) cc_final: 0.8543 (p) REVERT: C 70 THR cc_start: 0.8574 (t) cc_final: 0.8159 (p) REVERT: D 82 VAL cc_start: 0.9000 (p) cc_final: 0.8651 (t) REVERT: D 108 GLN cc_start: 0.8783 (tt0) cc_final: 0.8489 (tt0) REVERT: D 149 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 151 ARG cc_start: 0.8734 (ptt180) cc_final: 0.6885 (ttt180) REVERT: D 172 ASP cc_start: 0.8325 (t0) cc_final: 0.8105 (t70) REVERT: D 271 PHE cc_start: 0.8813 (p90) cc_final: 0.8519 (p90) REVERT: D 275 ASN cc_start: 0.8524 (t0) cc_final: 0.8309 (t0) REVERT: D 304 PHE cc_start: 0.8562 (p90) cc_final: 0.8186 (p90) REVERT: D 371 THR cc_start: 0.8472 (p) cc_final: 0.7800 (t) REVERT: D 373 MET cc_start: 0.8367 (mmm) cc_final: 0.7832 (mmm) REVERT: D 387 ASN cc_start: 0.8211 (t0) cc_final: 0.7143 (p0) REVERT: D 389 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7597 (mm-40) REVERT: D 420 VAL cc_start: 0.8857 (t) cc_final: 0.8500 (m) REVERT: D 466 VAL cc_start: 0.8754 (t) cc_final: 0.8485 (p) REVERT: D 511 GLN cc_start: 0.8734 (mt0) cc_final: 0.7790 (mt0) outliers start: 34 outliers final: 28 residues processed: 289 average time/residue: 0.0873 time to fit residues: 36.4785 Evaluate side-chains 300 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 126 SER 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 249 THR 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 189 THR 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 312 VAL Chi-restraints excluded: chain D residue 339 MET Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.097932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.084919 restraints weight = 17206.397| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.52 r_work: 0.2845 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3211 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= 0.115 Angle : 0.570 11.939 14166 Z= 0.284 Chirality : 0.047 0.195 1582 Planarity : 0.005 0.042 1869 Dihedral : 4.084 19.279 1422 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.76 % Allowed : 19.82 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.22), residues: 1320 helix: -0.05 (0.84), residues: 50 sheet: 0.26 (0.27), residues: 382 loop : -0.82 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.025 0.001 TYR B 369 PHE 0.011 0.001 PHE B 78 TRP 0.059 0.002 TRP D 316 HIS 0.004 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00274 (10319) covalent geometry : angle 0.56991 (14166) hydrogen bonds : bond 0.03316 ( 292) hydrogen bonds : angle 6.10342 ( 741) ********************** 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 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.381 Fit side-chains REVERT: A 123 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8475 (m) REVERT: A 206 THR cc_start: 0.8916 (m) cc_final: 0.8453 (p) REVERT: B 74 TYR cc_start: 0.8818 (t80) cc_final: 0.8351 (t80) REVERT: B 75 ASN cc_start: 0.8384 (t0) cc_final: 0.8133 (t0) REVERT: B 143 GLU cc_start: 0.8240 (pp20) cc_final: 0.7899 (pp20) REVERT: B 149 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 168 ILE cc_start: 0.8423 (tp) cc_final: 0.8174 (tt) REVERT: B 219 GLU cc_start: 0.7710 (mp0) cc_final: 0.7228 (mp0) REVERT: B 249 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7836 (t) REVERT: B 295 ILE cc_start: 0.8325 (mt) cc_final: 0.7933 (mt) REVERT: B 338 ASP cc_start: 0.8177 (p0) cc_final: 0.7789 (p0) REVERT: B 349 ILE cc_start: 0.8343 (mp) cc_final: 0.8134 (mm) REVERT: B 357 PHE cc_start: 0.8275 (m-80) cc_final: 0.8071 (m-80) REVERT: B 372 THR cc_start: 0.8438 (p) cc_final: 0.8047 (t) REVERT: B 373 MET cc_start: 0.8785 (mmp) cc_final: 0.8281 (mmp) REVERT: B 377 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 413 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7958 (mp10) REVERT: B 444 VAL cc_start: 0.8950 (t) cc_final: 0.8676 (m) REVERT: B 481 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6672 (t0) REVERT: B 518 ASN cc_start: 0.8101 (m-40) cc_final: 0.7658 (t0) REVERT: B 546 ASP cc_start: 0.8033 (t70) cc_final: 0.7784 (t0) REVERT: B 548 SER cc_start: 0.8477 (m) cc_final: 0.8165 (p) REVERT: B 566 VAL cc_start: 0.8797 (t) cc_final: 0.8422 (p) REVERT: C 70 THR cc_start: 0.8539 (t) cc_final: 0.8126 (p) REVERT: D 108 GLN cc_start: 0.8766 (tt0) cc_final: 0.8446 (tt0) REVERT: D 149 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 151 ARG cc_start: 0.8694 (ptt180) cc_final: 0.6832 (ttt180) REVERT: D 271 PHE cc_start: 0.8839 (p90) cc_final: 0.8535 (p90) REVERT: D 304 PHE cc_start: 0.8466 (p90) cc_final: 0.8156 (p90) REVERT: D 373 MET cc_start: 0.8382 (mmm) cc_final: 0.7882 (mmm) REVERT: D 387 ASN cc_start: 0.8182 (t0) cc_final: 0.6974 (p0) REVERT: D 389 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7585 (mm-40) REVERT: D 420 VAL cc_start: 0.8696 (t) cc_final: 0.8356 (m) REVERT: D 421 MET cc_start: 0.8409 (mmt) cc_final: 0.8170 (mmm) REVERT: D 428 THR cc_start: 0.8622 (p) cc_final: 0.8377 (t) REVERT: D 511 GLN cc_start: 0.8740 (mt0) cc_final: 0.7786 (mt0) outliers start: 30 outliers final: 23 residues processed: 278 average time/residue: 0.0910 time to fit residues: 36.6350 Evaluate side-chains 289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 126 SER 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 249 THR 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 189 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 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 372 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.098365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085341 restraints weight = 17150.988| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.51 r_work: 0.2869 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10319 Z= 0.130 Angle : 0.572 11.910 14166 Z= 0.283 Chirality : 0.047 0.165 1582 Planarity : 0.005 0.041 1869 Dihedral : 4.061 18.573 1422 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.32 % Allowed : 19.45 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1320 helix: -0.09 (0.83), residues: 50 sheet: 0.27 (0.27), residues: 382 loop : -0.81 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 216 TYR 0.014 0.001 TYR B 369 PHE 0.016 0.001 PHE C 72 TRP 0.049 0.002 TRP D 316 HIS 0.004 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00309 (10319) covalent geometry : angle 0.57205 (14166) hydrogen bonds : bond 0.03497 ( 292) hydrogen bonds : angle 6.08800 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.76 seconds wall clock time: 40 minutes 48.07 seconds (2448.07 seconds total)