Starting phenix.real_space_refine on Fri Nov 15 22:43:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_61528.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_61528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_61528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_61528.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jji_61528/11_2024/9jji_61528.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6407 2.51 5 N 1679 2.21 5 O 1901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10021 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 16, 'TRANS': 151} Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3673 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 447} Chain breaks: 2 Chain: "C" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 16, 'TRANS': 151} Chain: "D" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3752 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459} Time building chain proxies: 6.05, per 1000 atoms: 0.60 Number of scatterers: 10021 At special positions: 0 Unit cell: (116.62, 112.504, 116.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1901 8.00 N 1679 7.00 C 6407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 20 sheets defined 11.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.557A pdb=" N ARG A 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 100 through 107 removed outlier: 4.004A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.571A pdb=" N ARG B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.527A pdb=" N ASN B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.826A pdb=" N LEU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.937A pdb=" N ILE B 443 " --> pdb=" O PRO B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.013A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.632A pdb=" N ARG C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 70 " --> pdb=" O THR C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 70' Processing helix chain 'C' and resid 96 through 99 Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.995A pdb=" N VAL C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.777A pdb=" N ARG D 69 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.619A pdb=" N ASN D 100 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.703A pdb=" N LEU D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.921A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 5.834A pdb=" N TYR A 74 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR A 215 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 76 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.120A pdb=" N ILE A 89 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 194 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 91 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG A 132 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN A 197 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 130 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 81 removed outlier: 5.838A pdb=" N TYR B 74 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR B 215 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.673A pdb=" N LEU B 192 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B 92 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 190 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 132 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 197 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY B 130 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA7, first strand: chain 'B' and resid 485 through 488 removed outlier: 4.882A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 522 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 516 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 518 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 553 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 546 removed outlier: 7.674A pdb=" N ILE B 261 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL B 466 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 390 removed outlier: 4.463A pdb=" N TRP B 354 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.019A pdb=" N SER B 319 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N ARG B 299 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 420 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 416 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B 301 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR B 414 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 6.916A pdb=" N VAL C 213 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 77 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 211 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR C 79 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 209 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 94 removed outlier: 7.035A pdb=" N ILE C 89 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 194 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR C 91 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG C 132 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 197 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY C 130 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AB5, first strand: chain 'D' and resid 73 through 81 removed outlier: 5.904A pdb=" N TYR D 74 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N THR D 215 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN D 210 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 94 removed outlier: 6.717A pdb=" N LEU D 192 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR D 92 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 190 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG D 132 " --> pdb=" O TYR D 195 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN D 197 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY D 130 " --> pdb=" O ASN D 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AB8, first strand: chain 'D' and resid 485 through 488 removed outlier: 5.013A pdb=" N PHE D 534 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE D 512 " --> pdb=" O PRO D 558 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 514 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP D 552 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 545 through 546 removed outlier: 7.643A pdb=" N ILE D 261 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL D 466 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE D 534 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 523 " --> pdb=" O ASN D 568 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 295 through 297 removed outlier: 9.696A pdb=" N TRP D 354 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N ALA D 375 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N GLY D 356 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N MET D 373 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLY D 358 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR D 371 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE D 360 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.900A pdb=" N ILE D 360 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR D 371 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLY D 358 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N MET D 373 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N GLY D 356 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N ALA D 375 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N TRP D 354 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY D 353 " --> pdb=" O SER D 427 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 3.14 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.270 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10319 Z= 0.301 Angle : 0.601 4.830 14166 Z= 0.325 Chirality : 0.047 0.135 1582 Planarity : 0.004 0.038 1869 Dihedral : 12.411 89.356 3598 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1320 helix: -0.62 (0.88), residues: 46 sheet: 0.32 (0.25), residues: 413 loop : -0.58 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 278 HIS 0.004 0.001 HIS D 179 PHE 0.019 0.002 PHE B 357 TYR 0.029 0.002 TYR C 195 ARG 0.005 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.144 Fit side-chains REVERT: A 93 VAL cc_start: 0.8219 (p) cc_final: 0.7776 (m) REVERT: A 128 VAL cc_start: 0.8462 (m) cc_final: 0.8201 (t) REVERT: A 206 THR cc_start: 0.8789 (m) cc_final: 0.8135 (p) REVERT: B 74 TYR cc_start: 0.8735 (t80) cc_final: 0.8204 (t80) REVERT: B 109 MET cc_start: 0.7960 (ptp) cc_final: 0.7720 (ptm) REVERT: B 143 GLU cc_start: 0.7686 (pp20) cc_final: 0.7388 (pp20) REVERT: B 149 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 161 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.8208 (ptt180) REVERT: B 168 ILE cc_start: 0.8379 (tp) cc_final: 0.8128 (tt) REVERT: B 170 MET cc_start: 0.7970 (ttm) cc_final: 0.7726 (ttp) REVERT: B 219 GLU cc_start: 0.6896 (mp0) cc_final: 0.6644 (mp0) REVERT: B 295 ILE cc_start: 0.8091 (mt) cc_final: 0.7755 (mt) REVERT: B 298 ASP cc_start: 0.7338 (p0) cc_final: 0.6884 (p0) REVERT: B 328 ILE cc_start: 0.9289 (tt) cc_final: 0.8881 (tt) REVERT: B 365 ASN cc_start: 0.8064 (p0) cc_final: 0.7582 (p0) REVERT: B 398 GLN cc_start: 0.8052 (mt0) cc_final: 0.7640 (mt0) REVERT: B 413 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7978 (mm-40) REVERT: B 455 ILE cc_start: 0.8249 (tp) cc_final: 0.7963 (pt) REVERT: B 530 VAL cc_start: 0.8835 (t) cc_final: 0.8629 (p) REVERT: B 535 TYR cc_start: 0.8601 (m-80) cc_final: 0.8131 (m-10) REVERT: B 546 ASP cc_start: 0.7500 (t70) cc_final: 0.7097 (t0) REVERT: B 548 SER cc_start: 0.8357 (m) cc_final: 0.7946 (p) REVERT: B 552 ASP cc_start: 0.7437 (p0) cc_final: 0.7072 (p0) REVERT: B 566 VAL cc_start: 0.8871 (t) cc_final: 0.8617 (m) REVERT: C 129 PHE cc_start: 0.8461 (m-80) cc_final: 0.7765 (m-80) REVERT: C 225 MET cc_start: 0.6588 (mtt) cc_final: 0.6378 (mtm) REVERT: D 151 ARG cc_start: 0.8311 (ptt180) cc_final: 0.6905 (ptm160) REVERT: D 152 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7581 (mt0) REVERT: D 210 GLN cc_start: 0.8068 (mm110) cc_final: 0.7820 (mm110) REVERT: D 260 GLU cc_start: 0.7159 (pt0) cc_final: 0.6925 (pt0) REVERT: D 271 PHE cc_start: 0.8727 (p90) cc_final: 0.8457 (p90) REVERT: D 344 PHE cc_start: 0.8440 (p90) cc_final: 0.8230 (p90) REVERT: D 362 ASN cc_start: 0.7929 (t0) cc_final: 0.7330 (t0) REVERT: D 364 SER cc_start: 0.8679 (m) cc_final: 0.8342 (p) REVERT: D 373 MET cc_start: 0.7772 (mmm) cc_final: 0.7340 (mmm) REVERT: D 377 GLU cc_start: 0.7951 (tt0) cc_final: 0.7344 (tt0) REVERT: D 389 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7169 (mm-40) REVERT: D 412 ASN cc_start: 0.7895 (m110) cc_final: 0.7528 (m110) REVERT: D 428 THR cc_start: 0.8215 (p) cc_final: 0.7906 (p) REVERT: D 435 THR cc_start: 0.7900 (p) cc_final: 0.7534 (t) REVERT: D 466 VAL cc_start: 0.8490 (t) cc_final: 0.8223 (p) REVERT: D 511 GLN cc_start: 0.8449 (mt0) cc_final: 0.7404 (mt0) REVERT: D 514 VAL cc_start: 0.8719 (t) cc_final: 0.8210 (p) REVERT: D 523 PHE cc_start: 0.8376 (p90) cc_final: 0.8005 (p90) REVERT: D 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7437 (m-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2157 time to fit residues: 87.5273 Evaluate side-chains 254 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 0.0010 chunk 118 optimal weight: 9.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 210 GLN B 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10319 Z= 0.244 Angle : 0.581 7.363 14166 Z= 0.296 Chirality : 0.048 0.175 1582 Planarity : 0.005 0.042 1869 Dihedral : 4.188 18.285 1422 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.47 % Allowed : 9.22 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1320 helix: -1.02 (0.78), residues: 50 sheet: 0.51 (0.25), residues: 404 loop : -0.72 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 316 HIS 0.006 0.002 HIS C 179 PHE 0.015 0.002 PHE B 78 TYR 0.014 0.002 TYR D 91 ARG 0.004 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 1.104 Fit side-chains REVERT: A 113 TRP cc_start: 0.8837 (p-90) cc_final: 0.8130 (p-90) REVERT: A 128 VAL cc_start: 0.8400 (m) cc_final: 0.8143 (t) REVERT: A 206 THR cc_start: 0.8815 (m) cc_final: 0.8193 (p) REVERT: B 74 TYR cc_start: 0.8633 (t80) cc_final: 0.8054 (t80) REVERT: B 143 GLU cc_start: 0.7684 (pp20) cc_final: 0.7408 (pp20) REVERT: B 161 ARG cc_start: 0.8464 (ptt-90) cc_final: 0.8160 (ptt180) REVERT: B 262 VAL cc_start: 0.8843 (m) cc_final: 0.8532 (t) REVERT: B 295 ILE cc_start: 0.7974 (mt) cc_final: 0.7647 (mt) REVERT: B 298 ASP cc_start: 0.7356 (p0) cc_final: 0.6950 (p0) REVERT: B 311 ASN cc_start: 0.8645 (m-40) cc_final: 0.8433 (m-40) REVERT: B 369 TYR cc_start: 0.7745 (m-10) cc_final: 0.7400 (m-10) REVERT: B 398 GLN cc_start: 0.7985 (mt0) cc_final: 0.7534 (mt0) REVERT: B 413 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7987 (mm-40) REVERT: B 444 VAL cc_start: 0.8582 (t) cc_final: 0.8207 (m) REVERT: B 455 ILE cc_start: 0.8241 (tp) cc_final: 0.7975 (pt) REVERT: B 546 ASP cc_start: 0.7364 (t70) cc_final: 0.7048 (t0) REVERT: B 548 SER cc_start: 0.8393 (m) cc_final: 0.8047 (p) REVERT: B 566 VAL cc_start: 0.8710 (t) cc_final: 0.8499 (m) REVERT: C 99 ASN cc_start: 0.7734 (m-40) cc_final: 0.7420 (m110) REVERT: D 151 ARG cc_start: 0.8295 (ptt180) cc_final: 0.6769 (ttt180) REVERT: D 152 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7313 (mm-40) REVERT: D 210 GLN cc_start: 0.8083 (mm110) cc_final: 0.7767 (mm110) REVERT: D 213 VAL cc_start: 0.7622 (t) cc_final: 0.7412 (m) REVERT: D 271 PHE cc_start: 0.8774 (p90) cc_final: 0.8370 (p90) REVERT: D 344 PHE cc_start: 0.8291 (p90) cc_final: 0.8024 (p90) REVERT: D 362 ASN cc_start: 0.8067 (t0) cc_final: 0.7467 (t0) REVERT: D 364 SER cc_start: 0.8698 (m) cc_final: 0.8295 (p) REVERT: D 373 MET cc_start: 0.7827 (mmm) cc_final: 0.7267 (mmm) REVERT: D 377 GLU cc_start: 0.7938 (tt0) cc_final: 0.7192 (tt0) REVERT: D 387 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.6685 (p0) REVERT: D 428 THR cc_start: 0.8379 (p) cc_final: 0.8053 (t) REVERT: D 466 VAL cc_start: 0.8462 (t) cc_final: 0.8115 (p) REVERT: D 511 GLN cc_start: 0.8535 (mt0) cc_final: 0.8200 (mt0) REVERT: D 514 VAL cc_start: 0.8504 (t) cc_final: 0.8210 (m) REVERT: D 523 PHE cc_start: 0.8180 (p90) cc_final: 0.7845 (p90) REVERT: D 549 ASP cc_start: 0.7564 (m-30) cc_final: 0.7337 (m-30) REVERT: D 566 VAL cc_start: 0.8248 (t) cc_final: 0.7918 (t) outliers start: 16 outliers final: 15 residues processed: 264 average time/residue: 0.2219 time to fit residues: 82.9919 Evaluate side-chains 256 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 95 optimal weight: 8.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10319 Z= 0.158 Angle : 0.524 6.919 14166 Z= 0.263 Chirality : 0.046 0.140 1582 Planarity : 0.004 0.039 1869 Dihedral : 3.910 17.091 1422 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.03 % Allowed : 11.61 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1320 helix: -0.85 (0.80), residues: 50 sheet: 0.63 (0.26), residues: 394 loop : -0.71 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 68 HIS 0.003 0.001 HIS D 277 PHE 0.011 0.001 PHE B 78 TYR 0.010 0.001 TYR D 91 ARG 0.003 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8821 (p-90) cc_final: 0.8158 (p-90) REVERT: A 128 VAL cc_start: 0.8391 (m) cc_final: 0.8154 (t) REVERT: A 206 THR cc_start: 0.8755 (m) cc_final: 0.8117 (p) REVERT: B 74 TYR cc_start: 0.8643 (t80) cc_final: 0.8034 (t80) REVERT: B 143 GLU cc_start: 0.7690 (pp20) cc_final: 0.7423 (pp20) REVERT: B 249 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7684 (t) REVERT: B 295 ILE cc_start: 0.7970 (mt) cc_final: 0.7644 (mt) REVERT: B 298 ASP cc_start: 0.7410 (p0) cc_final: 0.6852 (p0) REVERT: B 299 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6821 (mmm-85) REVERT: B 311 ASN cc_start: 0.8642 (m-40) cc_final: 0.8380 (m-40) REVERT: B 369 TYR cc_start: 0.7724 (m-10) cc_final: 0.7487 (m-10) REVERT: B 372 THR cc_start: 0.8311 (p) cc_final: 0.7751 (t) REVERT: B 387 ASN cc_start: 0.6970 (t0) cc_final: 0.6417 (t0) REVERT: B 398 GLN cc_start: 0.7896 (mt0) cc_final: 0.7508 (mt0) REVERT: B 413 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7949 (mm-40) REVERT: B 427 SER cc_start: 0.8107 (p) cc_final: 0.7769 (p) REVERT: B 444 VAL cc_start: 0.8611 (t) cc_final: 0.8230 (m) REVERT: B 546 ASP cc_start: 0.7359 (t70) cc_final: 0.7079 (t0) REVERT: B 548 SER cc_start: 0.8367 (m) cc_final: 0.7979 (p) REVERT: C 129 PHE cc_start: 0.8546 (m-80) cc_final: 0.7911 (m-80) REVERT: C 176 ASN cc_start: 0.8251 (m-40) cc_final: 0.8006 (m-40) REVERT: C 177 MET cc_start: 0.7200 (mmt) cc_final: 0.6602 (mmt) REVERT: D 151 ARG cc_start: 0.8326 (ptt180) cc_final: 0.6779 (ttt180) REVERT: D 152 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7456 (mm-40) REVERT: D 177 MET cc_start: 0.7683 (mmm) cc_final: 0.6727 (mmt) REVERT: D 210 GLN cc_start: 0.8048 (mm110) cc_final: 0.7733 (mm110) REVERT: D 213 VAL cc_start: 0.7604 (t) cc_final: 0.7385 (m) REVERT: D 271 PHE cc_start: 0.8801 (p90) cc_final: 0.8486 (p90) REVERT: D 344 PHE cc_start: 0.8294 (p90) cc_final: 0.7951 (p90) REVERT: D 362 ASN cc_start: 0.8118 (t0) cc_final: 0.7521 (t0) REVERT: D 364 SER cc_start: 0.8691 (m) cc_final: 0.8319 (p) REVERT: D 373 MET cc_start: 0.7813 (mmm) cc_final: 0.7271 (mmm) REVERT: D 377 GLU cc_start: 0.7905 (tt0) cc_final: 0.7175 (tt0) REVERT: D 380 PHE cc_start: 0.7943 (m-80) cc_final: 0.7633 (m-80) REVERT: D 387 ASN cc_start: 0.7805 (t0) cc_final: 0.6940 (p0) REVERT: D 420 VAL cc_start: 0.8375 (t) cc_final: 0.8029 (m) REVERT: D 428 THR cc_start: 0.8425 (p) cc_final: 0.8165 (t) REVERT: D 432 SER cc_start: 0.8126 (m) cc_final: 0.7886 (t) REVERT: D 466 VAL cc_start: 0.8383 (t) cc_final: 0.8028 (p) REVERT: D 490 GLN cc_start: 0.8614 (mt0) cc_final: 0.8394 (mt0) REVERT: D 511 GLN cc_start: 0.8520 (mt0) cc_final: 0.7489 (mt0) REVERT: D 514 VAL cc_start: 0.8543 (t) cc_final: 0.8223 (m) REVERT: D 523 PHE cc_start: 0.8087 (p90) cc_final: 0.7756 (p90) REVERT: D 525 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6733 (mt-10) REVERT: D 566 VAL cc_start: 0.8346 (t) cc_final: 0.7783 (m) outliers start: 22 outliers final: 15 residues processed: 265 average time/residue: 0.2236 time to fit residues: 83.3884 Evaluate side-chains 265 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS D 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10319 Z= 0.456 Angle : 0.649 7.496 14166 Z= 0.338 Chirality : 0.051 0.168 1582 Planarity : 0.006 0.049 1869 Dihedral : 4.594 19.370 1422 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.13 % Allowed : 12.90 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1320 helix: -1.24 (0.75), residues: 50 sheet: 0.23 (0.25), residues: 398 loop : -0.86 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 68 HIS 0.007 0.002 HIS C 179 PHE 0.021 0.002 PHE D 223 TYR 0.020 0.002 TYR B 74 ARG 0.004 0.001 ARG B 69 *********************** 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 296 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 206 THR cc_start: 0.8874 (m) cc_final: 0.8524 (t) REVERT: B 74 TYR cc_start: 0.8700 (t80) cc_final: 0.8249 (t80) REVERT: B 75 ASN cc_start: 0.8323 (t0) cc_final: 0.7918 (t0) REVERT: B 149 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6452 (mm-30) REVERT: B 219 GLU cc_start: 0.6919 (mp0) cc_final: 0.6643 (mp0) REVERT: B 257 TRP cc_start: 0.8922 (m100) cc_final: 0.8711 (m100) REVERT: B 295 ILE cc_start: 0.8097 (mt) cc_final: 0.7737 (mt) REVERT: B 298 ASP cc_start: 0.7605 (p0) cc_final: 0.7159 (p0) REVERT: B 349 ILE cc_start: 0.8286 (mp) cc_final: 0.8074 (mm) REVERT: B 369 TYR cc_start: 0.7911 (m-10) cc_final: 0.7459 (m-10) REVERT: B 372 THR cc_start: 0.8350 (p) cc_final: 0.7849 (t) REVERT: B 377 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7328 (tm-30) REVERT: B 398 GLN cc_start: 0.7974 (mt0) cc_final: 0.7464 (mt0) REVERT: B 413 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7961 (mm-40) REVERT: B 444 VAL cc_start: 0.8739 (t) cc_final: 0.8414 (m) REVERT: B 546 ASP cc_start: 0.7345 (t70) cc_final: 0.7126 (t0) REVERT: B 548 SER cc_start: 0.8363 (m) cc_final: 0.8059 (p) REVERT: D 82 VAL cc_start: 0.8922 (p) cc_final: 0.8558 (t) REVERT: D 149 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7107 (mm-30) REVERT: D 151 ARG cc_start: 0.8398 (ptt180) cc_final: 0.6829 (ttt180) REVERT: D 152 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7468 (mm-40) REVERT: D 271 PHE cc_start: 0.8813 (p90) cc_final: 0.8445 (p90) REVERT: D 275 ASN cc_start: 0.8129 (t0) cc_final: 0.7754 (t0) REVERT: D 304 PHE cc_start: 0.8251 (p90) cc_final: 0.7934 (p90) REVERT: D 344 PHE cc_start: 0.8337 (p90) cc_final: 0.7811 (p90) REVERT: D 362 ASN cc_start: 0.8191 (t0) cc_final: 0.7548 (t0) REVERT: D 364 SER cc_start: 0.8650 (m) cc_final: 0.8293 (p) REVERT: D 371 THR cc_start: 0.8131 (p) cc_final: 0.7444 (t) REVERT: D 373 MET cc_start: 0.7799 (mmm) cc_final: 0.6868 (mmm) REVERT: D 377 GLU cc_start: 0.7880 (tt0) cc_final: 0.7064 (tt0) REVERT: D 387 ASN cc_start: 0.8123 (t0) cc_final: 0.7325 (p0) REVERT: D 389 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7370 (mm-40) REVERT: D 428 THR cc_start: 0.8518 (p) cc_final: 0.8263 (t) REVERT: D 466 VAL cc_start: 0.8503 (t) cc_final: 0.8246 (p) REVERT: D 511 GLN cc_start: 0.8504 (mt0) cc_final: 0.7498 (mt0) REVERT: D 514 VAL cc_start: 0.8593 (t) cc_final: 0.8239 (m) REVERT: D 523 PHE cc_start: 0.8218 (p90) cc_final: 0.7895 (p90) REVERT: D 525 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6585 (mt-10) REVERT: D 566 VAL cc_start: 0.8355 (t) cc_final: 0.7700 (m) outliers start: 34 outliers final: 29 residues processed: 276 average time/residue: 0.2112 time to fit residues: 82.7166 Evaluate side-chains 281 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 428 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 199 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS D 95 HIS D 265 GLN D 389 GLN D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10319 Z= 0.189 Angle : 0.541 8.836 14166 Z= 0.273 Chirality : 0.047 0.195 1582 Planarity : 0.005 0.040 1869 Dihedral : 4.167 19.061 1422 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.04 % Allowed : 14.84 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1320 helix: -0.75 (0.79), residues: 50 sheet: 0.33 (0.25), residues: 396 loop : -0.88 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 68 HIS 0.003 0.001 HIS D 277 PHE 0.011 0.001 PHE B 78 TYR 0.014 0.001 TYR D 91 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8827 (p-90) cc_final: 0.8132 (p-90) REVERT: A 206 THR cc_start: 0.8864 (m) cc_final: 0.8459 (t) REVERT: B 74 TYR cc_start: 0.8636 (t80) cc_final: 0.8166 (t80) REVERT: B 75 ASN cc_start: 0.8258 (t0) cc_final: 0.7959 (t0) REVERT: B 149 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6447 (mm-30) REVERT: B 177 MET cc_start: 0.8611 (mmm) cc_final: 0.8327 (mmp) REVERT: B 219 GLU cc_start: 0.6843 (mp0) cc_final: 0.6583 (mp0) REVERT: B 249 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7662 (t) REVERT: B 257 TRP cc_start: 0.8861 (m100) cc_final: 0.8607 (m100) REVERT: B 260 GLU cc_start: 0.7077 (tt0) cc_final: 0.6844 (tt0) REVERT: B 295 ILE cc_start: 0.8033 (mt) cc_final: 0.7646 (mt) REVERT: B 298 ASP cc_start: 0.7571 (p0) cc_final: 0.7151 (p0) REVERT: B 339 MET cc_start: 0.7868 (mtp) cc_final: 0.7554 (mtp) REVERT: B 369 TYR cc_start: 0.7739 (m-10) cc_final: 0.7350 (m-10) REVERT: B 372 THR cc_start: 0.8334 (p) cc_final: 0.7855 (t) REVERT: B 373 MET cc_start: 0.8340 (mmp) cc_final: 0.7762 (mmp) REVERT: B 377 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 413 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7946 (mm-40) REVERT: B 444 VAL cc_start: 0.8729 (t) cc_final: 0.8404 (m) REVERT: B 481 ASN cc_start: 0.6839 (OUTLIER) cc_final: 0.6543 (t160) REVERT: B 546 ASP cc_start: 0.7339 (t70) cc_final: 0.7119 (t0) REVERT: B 548 SER cc_start: 0.8321 (m) cc_final: 0.7900 (p) REVERT: D 149 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7044 (mm-30) REVERT: D 151 ARG cc_start: 0.8370 (ptt180) cc_final: 0.7014 (ptm160) REVERT: D 271 PHE cc_start: 0.8826 (p90) cc_final: 0.8444 (p90) REVERT: D 275 ASN cc_start: 0.8270 (t0) cc_final: 0.8026 (t0) REVERT: D 291 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7538 (ttp-110) REVERT: D 304 PHE cc_start: 0.8156 (p90) cc_final: 0.7814 (p90) REVERT: D 316 TRP cc_start: 0.8370 (t60) cc_final: 0.7896 (t60) REVERT: D 344 PHE cc_start: 0.8323 (p90) cc_final: 0.7747 (p90) REVERT: D 362 ASN cc_start: 0.8165 (t0) cc_final: 0.7556 (t0) REVERT: D 364 SER cc_start: 0.8672 (m) cc_final: 0.8288 (p) REVERT: D 373 MET cc_start: 0.7820 (mmm) cc_final: 0.7100 (mmm) REVERT: D 377 GLU cc_start: 0.7875 (tt0) cc_final: 0.7098 (tt0) REVERT: D 387 ASN cc_start: 0.7905 (t0) cc_final: 0.7076 (p0) REVERT: D 389 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: D 412 ASN cc_start: 0.8182 (m-40) cc_final: 0.7646 (m-40) REVERT: D 428 THR cc_start: 0.8510 (p) cc_final: 0.8253 (t) REVERT: D 466 VAL cc_start: 0.8382 (t) cc_final: 0.8062 (p) REVERT: D 490 GLN cc_start: 0.8502 (mt0) cc_final: 0.8237 (mt0) REVERT: D 511 GLN cc_start: 0.8514 (mt0) cc_final: 0.7463 (mt0) REVERT: D 525 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 566 VAL cc_start: 0.8284 (t) cc_final: 0.7647 (m) outliers start: 33 outliers final: 23 residues processed: 290 average time/residue: 0.2131 time to fit residues: 87.6052 Evaluate side-chains 293 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 389 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 445 ASN Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.0270 chunk 114 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 31 optimal weight: 0.0870 chunk 126 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS B 516 GLN D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10319 Z= 0.125 Angle : 0.517 9.715 14166 Z= 0.257 Chirality : 0.046 0.149 1582 Planarity : 0.004 0.042 1869 Dihedral : 3.845 16.232 1422 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.58 % Allowed : 16.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1320 helix: -0.38 (0.83), residues: 50 sheet: 0.43 (0.26), residues: 387 loop : -0.78 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 68 HIS 0.002 0.000 HIS D 277 PHE 0.021 0.001 PHE D 523 TYR 0.009 0.001 TYR D 436 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8766 (p-90) cc_final: 0.8119 (p-90) REVERT: A 206 THR cc_start: 0.8799 (m) cc_final: 0.8360 (t) REVERT: B 74 TYR cc_start: 0.8583 (t80) cc_final: 0.8088 (t80) REVERT: B 177 MET cc_start: 0.8577 (mmm) cc_final: 0.8343 (mmp) REVERT: B 249 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7697 (t) REVERT: B 257 TRP cc_start: 0.8836 (m100) cc_final: 0.8548 (m100) REVERT: B 295 ILE cc_start: 0.7995 (mt) cc_final: 0.7613 (mt) REVERT: B 298 ASP cc_start: 0.7538 (p0) cc_final: 0.7018 (p0) REVERT: B 339 MET cc_start: 0.7743 (mtp) cc_final: 0.7471 (mtp) REVERT: B 357 PHE cc_start: 0.8106 (m-80) cc_final: 0.7895 (m-80) REVERT: B 372 THR cc_start: 0.8276 (p) cc_final: 0.7836 (t) REVERT: B 373 MET cc_start: 0.8318 (mmp) cc_final: 0.7762 (mmp) REVERT: B 413 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7933 (mm-40) REVERT: B 427 SER cc_start: 0.8155 (p) cc_final: 0.7952 (p) REVERT: B 444 VAL cc_start: 0.8720 (t) cc_final: 0.8383 (m) REVERT: B 481 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6490 (t160) REVERT: B 546 ASP cc_start: 0.7327 (t70) cc_final: 0.7112 (t0) REVERT: B 548 SER cc_start: 0.8294 (m) cc_final: 0.7938 (p) REVERT: C 72 PHE cc_start: 0.8205 (m-80) cc_final: 0.7821 (m-80) REVERT: D 151 ARG cc_start: 0.8332 (ptt180) cc_final: 0.7018 (ptm160) REVERT: D 177 MET cc_start: 0.7415 (mmp) cc_final: 0.7142 (mmm) REVERT: D 213 VAL cc_start: 0.7666 (t) cc_final: 0.7405 (p) REVERT: D 257 TRP cc_start: 0.8722 (m100) cc_final: 0.7440 (m100) REVERT: D 271 PHE cc_start: 0.8841 (p90) cc_final: 0.8473 (p90) REVERT: D 304 PHE cc_start: 0.8115 (p90) cc_final: 0.7888 (p90) REVERT: D 344 PHE cc_start: 0.8330 (p90) cc_final: 0.7712 (p90) REVERT: D 362 ASN cc_start: 0.8153 (t0) cc_final: 0.7568 (t0) REVERT: D 364 SER cc_start: 0.8686 (m) cc_final: 0.8307 (p) REVERT: D 372 THR cc_start: 0.8403 (p) cc_final: 0.7865 (t) REVERT: D 373 MET cc_start: 0.7815 (mmm) cc_final: 0.7372 (mmm) REVERT: D 377 GLU cc_start: 0.7837 (tt0) cc_final: 0.7082 (tt0) REVERT: D 380 PHE cc_start: 0.7756 (m-80) cc_final: 0.7479 (m-80) REVERT: D 387 ASN cc_start: 0.7984 (t0) cc_final: 0.7213 (p0) REVERT: D 389 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: D 413 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: D 428 THR cc_start: 0.8514 (p) cc_final: 0.8241 (t) REVERT: D 466 VAL cc_start: 0.8271 (t) cc_final: 0.7933 (p) REVERT: D 490 GLN cc_start: 0.8479 (mt0) cc_final: 0.8184 (mt0) REVERT: D 511 GLN cc_start: 0.8538 (mt0) cc_final: 0.7537 (mt0) REVERT: D 525 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6641 (mt-10) REVERT: D 566 VAL cc_start: 0.8354 (t) cc_final: 0.7734 (m) outliers start: 28 outliers final: 19 residues processed: 275 average time/residue: 0.2140 time to fit residues: 83.4621 Evaluate side-chains 280 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 413 GLN 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 549 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 GLN B 518 ASN C 99 ASN D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10319 Z= 0.205 Angle : 0.535 10.380 14166 Z= 0.267 Chirality : 0.047 0.138 1582 Planarity : 0.005 0.038 1869 Dihedral : 3.894 16.809 1422 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.69 % Allowed : 16.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1320 helix: -0.31 (0.82), residues: 50 sheet: 0.33 (0.26), residues: 400 loop : -0.73 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 68 HIS 0.004 0.001 HIS C 179 PHE 0.023 0.001 PHE D 523 TYR 0.013 0.001 TYR D 91 ARG 0.005 0.000 ARG C 132 *********************** 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 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8806 (p-90) cc_final: 0.8150 (p-90) REVERT: A 123 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8384 (m) REVERT: A 134 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 206 THR cc_start: 0.8817 (m) cc_final: 0.8379 (t) REVERT: B 74 TYR cc_start: 0.8604 (t80) cc_final: 0.8103 (t80) REVERT: B 149 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6396 (mm-30) REVERT: B 177 MET cc_start: 0.8601 (mmm) cc_final: 0.8341 (mmp) REVERT: B 219 GLU cc_start: 0.6840 (mp0) cc_final: 0.6577 (mp0) REVERT: B 249 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7708 (t) REVERT: B 257 TRP cc_start: 0.8873 (m100) cc_final: 0.8557 (m100) REVERT: B 295 ILE cc_start: 0.8047 (mt) cc_final: 0.7655 (mt) REVERT: B 298 ASP cc_start: 0.7551 (p0) cc_final: 0.7135 (p0) REVERT: B 339 MET cc_start: 0.7834 (mtp) cc_final: 0.7529 (mtp) REVERT: B 357 PHE cc_start: 0.8145 (m-80) cc_final: 0.7938 (m-80) REVERT: B 369 TYR cc_start: 0.7711 (m-10) cc_final: 0.7353 (m-10) REVERT: B 372 THR cc_start: 0.8301 (p) cc_final: 0.7849 (t) REVERT: B 373 MET cc_start: 0.8279 (mmp) cc_final: 0.7706 (mmp) REVERT: B 377 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 413 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7947 (mm-40) REVERT: B 427 SER cc_start: 0.8010 (p) cc_final: 0.7732 (p) REVERT: B 444 VAL cc_start: 0.8740 (t) cc_final: 0.8426 (m) REVERT: B 481 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6525 (t160) REVERT: B 546 ASP cc_start: 0.7335 (t70) cc_final: 0.7119 (t0) REVERT: B 548 SER cc_start: 0.8291 (m) cc_final: 0.7949 (p) REVERT: C 72 PHE cc_start: 0.8219 (m-80) cc_final: 0.7847 (m-80) REVERT: C 202 PHE cc_start: 0.7926 (m-80) cc_final: 0.7486 (m-80) REVERT: D 149 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7004 (mm-30) REVERT: D 151 ARG cc_start: 0.8345 (ptt180) cc_final: 0.6802 (ttt180) REVERT: D 177 MET cc_start: 0.7553 (mmp) cc_final: 0.7230 (mmm) REVERT: D 271 PHE cc_start: 0.8824 (p90) cc_final: 0.8483 (p90) REVERT: D 304 PHE cc_start: 0.8098 (p90) cc_final: 0.7856 (p90) REVERT: D 344 PHE cc_start: 0.8339 (p90) cc_final: 0.7702 (p90) REVERT: D 362 ASN cc_start: 0.8148 (t0) cc_final: 0.7572 (t0) REVERT: D 364 SER cc_start: 0.8683 (m) cc_final: 0.8302 (p) REVERT: D 372 THR cc_start: 0.8419 (p) cc_final: 0.7887 (t) REVERT: D 373 MET cc_start: 0.7770 (mmm) cc_final: 0.7095 (mmm) REVERT: D 377 GLU cc_start: 0.7846 (tt0) cc_final: 0.7077 (tt0) REVERT: D 380 PHE cc_start: 0.7810 (m-80) cc_final: 0.7535 (m-80) REVERT: D 387 ASN cc_start: 0.8002 (t0) cc_final: 0.7252 (p0) REVERT: D 389 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7484 (mm-40) REVERT: D 413 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7712 (mm-40) REVERT: D 428 THR cc_start: 0.8530 (p) cc_final: 0.8241 (t) REVERT: D 466 VAL cc_start: 0.8359 (t) cc_final: 0.8027 (p) REVERT: D 490 GLN cc_start: 0.8522 (mt0) cc_final: 0.8210 (mt0) REVERT: D 511 GLN cc_start: 0.8517 (mt0) cc_final: 0.7511 (mt0) REVERT: D 525 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6632 (mt-10) REVERT: D 566 VAL cc_start: 0.8356 (t) cc_final: 0.7723 (m) outliers start: 40 outliers final: 28 residues processed: 283 average time/residue: 0.2131 time to fit residues: 86.8398 Evaluate side-chains 294 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 134 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 481 ASN Chi-restraints excluded: chain C residue 79 THR 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 199 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 B 518 ASN C 99 ASN C 176 ASN D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10319 Z= 0.228 Angle : 0.548 11.233 14166 Z= 0.275 Chirality : 0.047 0.140 1582 Planarity : 0.005 0.039 1869 Dihedral : 3.968 17.146 1422 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.69 % Allowed : 16.41 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1320 helix: -0.34 (0.81), residues: 50 sheet: 0.27 (0.27), residues: 379 loop : -0.77 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 316 HIS 0.004 0.001 HIS C 179 PHE 0.024 0.001 PHE D 523 TYR 0.013 0.001 TYR D 91 ARG 0.003 0.000 ARG C 132 *********************** 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 306 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8799 (p-90) cc_final: 0.8102 (p-90) REVERT: A 123 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8371 (m) REVERT: A 134 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 206 THR cc_start: 0.8848 (m) cc_final: 0.8428 (t) REVERT: B 74 TYR cc_start: 0.8628 (t80) cc_final: 0.8106 (t80) REVERT: B 149 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6452 (mm-30) REVERT: B 177 MET cc_start: 0.8539 (mmm) cc_final: 0.8291 (mmp) REVERT: B 202 PHE cc_start: 0.7135 (m-10) cc_final: 0.6920 (m-10) REVERT: B 219 GLU cc_start: 0.6839 (mp0) cc_final: 0.6578 (mp0) REVERT: B 249 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7684 (t) REVERT: B 257 TRP cc_start: 0.8871 (m100) cc_final: 0.8555 (m100) REVERT: B 295 ILE cc_start: 0.8056 (mt) cc_final: 0.7679 (mt) REVERT: B 298 ASP cc_start: 0.7564 (p0) cc_final: 0.7149 (p0) REVERT: B 338 ASP cc_start: 0.7686 (p0) cc_final: 0.7198 (p0) REVERT: B 369 TYR cc_start: 0.7705 (m-10) cc_final: 0.7330 (m-10) REVERT: B 372 THR cc_start: 0.8322 (p) cc_final: 0.7870 (t) REVERT: B 373 MET cc_start: 0.8284 (mmp) cc_final: 0.7695 (mmp) REVERT: B 377 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7293 (tm-30) REVERT: B 413 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7944 (mm-40) REVERT: B 427 SER cc_start: 0.8111 (p) cc_final: 0.7894 (p) REVERT: B 444 VAL cc_start: 0.8817 (t) cc_final: 0.8498 (m) REVERT: B 481 ASN cc_start: 0.6894 (OUTLIER) cc_final: 0.6491 (t0) REVERT: B 546 ASP cc_start: 0.7324 (t70) cc_final: 0.7117 (t0) REVERT: B 548 SER cc_start: 0.8246 (m) cc_final: 0.7918 (p) REVERT: D 149 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7006 (mm-30) REVERT: D 151 ARG cc_start: 0.8345 (ptt180) cc_final: 0.6776 (ttt180) REVERT: D 177 MET cc_start: 0.7696 (mmp) cc_final: 0.7442 (mmm) REVERT: D 271 PHE cc_start: 0.8827 (p90) cc_final: 0.8486 (p90) REVERT: D 304 PHE cc_start: 0.8115 (p90) cc_final: 0.7871 (p90) REVERT: D 316 TRP cc_start: 0.8273 (t60) cc_final: 0.7978 (t60) REVERT: D 344 PHE cc_start: 0.8340 (p90) cc_final: 0.7674 (p90) REVERT: D 362 ASN cc_start: 0.8165 (t0) cc_final: 0.7557 (t0) REVERT: D 364 SER cc_start: 0.8677 (m) cc_final: 0.8299 (p) REVERT: D 372 THR cc_start: 0.8472 (p) cc_final: 0.8121 (t) REVERT: D 373 MET cc_start: 0.7805 (mmm) cc_final: 0.7267 (mmm) REVERT: D 377 GLU cc_start: 0.7854 (tt0) cc_final: 0.7078 (tt0) REVERT: D 380 PHE cc_start: 0.7841 (m-80) cc_final: 0.7536 (m-80) REVERT: D 387 ASN cc_start: 0.8017 (t0) cc_final: 0.7264 (p0) REVERT: D 389 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7527 (mm-40) REVERT: D 411 ILE cc_start: 0.8644 (mm) cc_final: 0.8308 (mp) REVERT: D 413 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7766 (mm-40) REVERT: D 428 THR cc_start: 0.8527 (p) cc_final: 0.8251 (t) REVERT: D 466 VAL cc_start: 0.8378 (t) cc_final: 0.8057 (p) REVERT: D 490 GLN cc_start: 0.8535 (mt0) cc_final: 0.8315 (mt0) REVERT: D 511 GLN cc_start: 0.8525 (mt0) cc_final: 0.7525 (mt0) REVERT: D 525 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6611 (mt-10) REVERT: D 566 VAL cc_start: 0.8345 (t) cc_final: 0.7715 (m) outliers start: 40 outliers final: 31 residues processed: 283 average time/residue: 0.2048 time to fit residues: 82.7096 Evaluate side-chains 302 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 134 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 481 ASN Chi-restraints excluded: chain B residue 518 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 199 ILE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 0.0570 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- 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 518 ASN C 99 ASN D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10319 Z= 0.142 Angle : 0.530 11.706 14166 Z= 0.264 Chirality : 0.046 0.160 1582 Planarity : 0.004 0.037 1869 Dihedral : 3.843 16.335 1422 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.13 % Allowed : 17.24 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1320 helix: -0.20 (0.82), residues: 50 sheet: 0.44 (0.27), residues: 383 loop : -0.71 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 316 HIS 0.003 0.001 HIS B 95 PHE 0.022 0.001 PHE D 523 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.000 ARG C 132 *********************** 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 296 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8764 (p-90) cc_final: 0.8078 (p-90) REVERT: A 123 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 134 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 206 THR cc_start: 0.8818 (m) cc_final: 0.8383 (t) REVERT: B 74 TYR cc_start: 0.8596 (t80) cc_final: 0.8087 (t80) REVERT: B 149 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6443 (mm-30) REVERT: B 151 ARG cc_start: 0.5436 (ptm160) cc_final: 0.5072 (ptm160) REVERT: B 177 MET cc_start: 0.8557 (mmm) cc_final: 0.8327 (mmp) REVERT: B 219 GLU cc_start: 0.6822 (mp0) cc_final: 0.6573 (mp0) REVERT: B 249 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7660 (t) REVERT: B 257 TRP cc_start: 0.8837 (m100) cc_final: 0.8524 (m100) REVERT: B 295 ILE cc_start: 0.8038 (mt) cc_final: 0.7662 (mt) REVERT: B 298 ASP cc_start: 0.7539 (p0) cc_final: 0.7135 (p0) REVERT: B 338 ASP cc_start: 0.7691 (p0) cc_final: 0.7192 (p0) REVERT: B 339 MET cc_start: 0.7784 (mtp) cc_final: 0.7504 (mtp) REVERT: B 369 TYR cc_start: 0.7649 (m-10) cc_final: 0.7323 (m-10) REVERT: B 372 THR cc_start: 0.8293 (p) cc_final: 0.7862 (t) REVERT: B 373 MET cc_start: 0.8274 (mmp) cc_final: 0.7698 (mmp) REVERT: B 377 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 413 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7929 (mm-40) REVERT: B 427 SER cc_start: 0.7875 (p) cc_final: 0.7648 (p) REVERT: B 444 VAL cc_start: 0.8813 (t) cc_final: 0.8495 (m) REVERT: B 481 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.6459 (t0) REVERT: B 546 ASP cc_start: 0.7330 (t70) cc_final: 0.7128 (t0) REVERT: B 548 SER cc_start: 0.8256 (m) cc_final: 0.7932 (p) REVERT: D 151 ARG cc_start: 0.8321 (ptt180) cc_final: 0.6777 (ttt180) REVERT: D 177 MET cc_start: 0.7619 (mmp) cc_final: 0.7381 (mmm) REVERT: D 271 PHE cc_start: 0.8826 (p90) cc_final: 0.8338 (p90) REVERT: D 304 PHE cc_start: 0.8080 (p90) cc_final: 0.7859 (p90) REVERT: D 344 PHE cc_start: 0.8311 (p90) cc_final: 0.7628 (p90) REVERT: D 362 ASN cc_start: 0.8172 (t0) cc_final: 0.7578 (t0) REVERT: D 364 SER cc_start: 0.8681 (m) cc_final: 0.8297 (p) REVERT: D 372 THR cc_start: 0.8407 (p) cc_final: 0.8038 (t) REVERT: D 373 MET cc_start: 0.7744 (mmm) cc_final: 0.7156 (mmm) REVERT: D 377 GLU cc_start: 0.7865 (tt0) cc_final: 0.7067 (tt0) REVERT: D 380 PHE cc_start: 0.7744 (m-80) cc_final: 0.7438 (m-80) REVERT: D 387 ASN cc_start: 0.8001 (t0) cc_final: 0.7267 (p0) REVERT: D 389 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7537 (mm-40) REVERT: D 411 ILE cc_start: 0.8640 (mm) cc_final: 0.8297 (mp) REVERT: D 413 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: D 428 THR cc_start: 0.8525 (p) cc_final: 0.8246 (t) REVERT: D 466 VAL cc_start: 0.8336 (t) cc_final: 0.7987 (p) REVERT: D 511 GLN cc_start: 0.8532 (mt0) cc_final: 0.7537 (mt0) REVERT: D 525 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6655 (mt-10) REVERT: D 566 VAL cc_start: 0.8323 (t) cc_final: 0.7708 (m) outliers start: 34 outliers final: 24 residues processed: 276 average time/residue: 0.2157 time to fit residues: 85.1671 Evaluate side-chains 293 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 THR 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 199 ILE 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 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 0.0030 chunk 86 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- 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 518 ASN D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10319 Z= 0.182 Angle : 0.540 12.214 14166 Z= 0.270 Chirality : 0.047 0.145 1582 Planarity : 0.005 0.038 1869 Dihedral : 3.869 16.515 1422 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.13 % Allowed : 17.24 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1320 helix: -0.08 (0.81), residues: 50 sheet: 0.49 (0.27), residues: 389 loop : -0.73 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 316 HIS 0.004 0.001 HIS B 95 PHE 0.022 0.001 PHE D 523 TYR 0.011 0.001 TYR D 91 ARG 0.004 0.000 ARG A 227 ********************** 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 296 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 113 TRP cc_start: 0.8757 (p-90) cc_final: 0.8078 (p-90) REVERT: A 123 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 134 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 206 THR cc_start: 0.8822 (m) cc_final: 0.8391 (t) REVERT: B 74 TYR cc_start: 0.8606 (t80) cc_final: 0.8097 (t80) REVERT: B 149 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6449 (mm-30) REVERT: B 177 MET cc_start: 0.8489 (mmm) cc_final: 0.8265 (mmp) REVERT: B 219 GLU cc_start: 0.6834 (mp0) cc_final: 0.6568 (mp0) REVERT: B 249 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7659 (t) REVERT: B 257 TRP cc_start: 0.8845 (m100) cc_final: 0.8532 (m100) REVERT: B 295 ILE cc_start: 0.8058 (mt) cc_final: 0.7686 (mt) REVERT: B 338 ASP cc_start: 0.7682 (p0) cc_final: 0.7182 (p0) REVERT: B 339 MET cc_start: 0.7812 (mtp) cc_final: 0.7510 (mtp) REVERT: B 369 TYR cc_start: 0.7659 (m-10) cc_final: 0.7323 (m-10) REVERT: B 372 THR cc_start: 0.8297 (p) cc_final: 0.7966 (t) REVERT: B 377 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 413 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 427 SER cc_start: 0.7879 (p) cc_final: 0.7646 (p) REVERT: B 444 VAL cc_start: 0.8823 (t) cc_final: 0.8510 (m) REVERT: B 481 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6537 (t0) REVERT: B 546 ASP cc_start: 0.7337 (t70) cc_final: 0.7126 (t0) REVERT: B 548 SER cc_start: 0.8192 (m) cc_final: 0.7867 (p) REVERT: D 151 ARG cc_start: 0.8323 (ptt180) cc_final: 0.6778 (ttt180) REVERT: D 177 MET cc_start: 0.7641 (mmp) cc_final: 0.7413 (mmm) REVERT: D 271 PHE cc_start: 0.8735 (p90) cc_final: 0.8453 (p90) REVERT: D 344 PHE cc_start: 0.8311 (p90) cc_final: 0.7623 (p90) REVERT: D 362 ASN cc_start: 0.8170 (t0) cc_final: 0.7582 (t0) REVERT: D 364 SER cc_start: 0.8676 (m) cc_final: 0.8294 (p) REVERT: D 372 THR cc_start: 0.8444 (p) cc_final: 0.8122 (t) REVERT: D 373 MET cc_start: 0.7730 (mmm) cc_final: 0.7258 (mmm) REVERT: D 377 GLU cc_start: 0.7862 (tt0) cc_final: 0.7060 (tt0) REVERT: D 380 PHE cc_start: 0.7763 (m-80) cc_final: 0.7460 (m-80) REVERT: D 387 ASN cc_start: 0.8009 (t0) cc_final: 0.7282 (p0) REVERT: D 389 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7562 (mm-40) REVERT: D 411 ILE cc_start: 0.8640 (mm) cc_final: 0.8312 (mp) REVERT: D 413 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: D 428 THR cc_start: 0.8525 (p) cc_final: 0.8241 (t) REVERT: D 466 VAL cc_start: 0.8349 (t) cc_final: 0.8002 (p) REVERT: D 511 GLN cc_start: 0.8538 (mt0) cc_final: 0.7540 (mt0) REVERT: D 525 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6658 (mt-10) REVERT: D 566 VAL cc_start: 0.8329 (t) cc_final: 0.7695 (m) outliers start: 34 outliers final: 27 residues processed: 277 average time/residue: 0.2109 time to fit residues: 83.0752 Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 THR 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 199 ILE 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 330 GLN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 265 GLN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085450 restraints weight = 17015.812| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.54 r_work: 0.2906 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10319 Z= 0.134 Angle : 0.534 11.994 14166 Z= 0.263 Chirality : 0.046 0.151 1582 Planarity : 0.004 0.037 1869 Dihedral : 3.754 16.001 1422 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.86 % Allowed : 18.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1320 helix: 0.10 (0.83), residues: 50 sheet: 0.51 (0.27), residues: 390 loop : -0.68 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 316 HIS 0.003 0.001 HIS B 95 PHE 0.021 0.001 PHE D 523 TYR 0.015 0.001 TYR D 567 ARG 0.003 0.000 ARG B 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.01 seconds wall clock time: 47 minutes 9.77 seconds (2829.77 seconds total)