Starting phenix.real_space_refine on Mon Mar 11 17:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydj_33749/03_2024/7ydj_33749.pdb" } resolution = 3.03 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= 0.001 sd= 0.021 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 60 5.16 5 C 5589 2.51 5 N 1507 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1744 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2194 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 5, 'TRANS': 268} Time building chain proxies: 5.06, per 1000 atoms: 0.58 Number of scatterers: 8751 At special positions: 0 Unit cell: (92.4, 119.9, 135.3, 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 60 16.00 O 1595 8.00 N 1507 7.00 C 5589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.12 Conformation dependent library (CDL) restraints added in 2.0 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.840A pdb=" N SER A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.611A pdb=" N SER A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.586A pdb=" N PHE A 272 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.838A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.755A pdb=" N TYR A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 364 removed outlier: 4.228A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 362 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.085A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.623A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.184A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.914A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 532 through 537 Processing helix chain 'R' and resid 544 through 572 Processing helix chain 'R' and resid 577 through 600 Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.888A pdb=" N ARG R 613 " --> pdb=" O GLY R 609 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.836A pdb=" N VAL R 662 " --> pdb=" O ILE R 658 " (cutoff:3.500A) Proline residue: R 663 - end of helix removed outlier: 3.515A pdb=" N TYR R 674 " --> pdb=" O SER R 670 " (cutoff:3.500A) Processing helix chain 'R' and resid 675 through 678 removed outlier: 4.009A pdb=" N TYR R 678 " --> pdb=" O SER R 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 675 through 678' Processing helix chain 'R' and resid 688 through 692 removed outlier: 3.514A pdb=" N GLY R 691 " --> pdb=" O PHE R 688 " (cutoff:3.500A) Processing helix chain 'R' and resid 693 through 726 removed outlier: 3.695A pdb=" N LEU R 697 " --> pdb=" O LEU R 693 " (cutoff:3.500A) Proline residue: R 699 - end of helix removed outlier: 3.532A pdb=" N PHE R 702 " --> pdb=" O GLY R 698 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS R 706 " --> pdb=" O PHE R 702 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER R 723 " --> pdb=" O THR R 719 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU R 724 " --> pdb=" O GLN R 720 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 749 removed outlier: 3.794A pdb=" N THR R 739 " --> pdb=" O ALA R 735 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE R 747 " --> pdb=" O ILE R 743 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU R 748 " --> pdb=" O ALA R 744 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 749 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 759 removed outlier: 3.932A pdb=" N ILE R 759 " --> pdb=" O GLY R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 776 removed outlier: 3.540A pdb=" N THR R 768 " --> pdb=" O SER R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 777 through 787 Processing helix chain 'R' and resid 790 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.261A pdb=" N VAL A 41 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 243 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 333 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.027A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.089A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.996A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.839A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.856A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 7.133A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.296A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.274A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1146 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: 2.61 Time building geometry restraints manager: 3.40 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: 2821 1.34 - 1.46: 2189 1.46 - 1.59: 3836 1.59 - 1.71: 0 1.71 - 1.83: 85 Bond restraints: 8931 Sorted by residual: bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.453 0.053 3.90e-02 6.57e+02 1.88e+00 bond pdb=" SD MET E 218 " pdb=" CE MET E 218 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.49e+00 bond pdb=" CB TRP R 716 " pdb=" CG TRP R 716 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.45e+00 bond pdb=" CG LEU R 562 " pdb=" CD2 LEU R 562 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" C ASP A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.14e+00 ... (remaining 8926 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.18: 89 104.18 - 111.67: 4181 111.67 - 119.16: 3085 119.16 - 126.64: 4594 126.64 - 134.13: 130 Bond angle restraints: 12079 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 113.39 108.56 4.83 1.47e+00 4.63e-01 1.08e+01 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.34 112.57 -4.23 1.31e+00 5.83e-01 1.04e+01 angle pdb=" C LEU B 252 " pdb=" N PHE B 253 " pdb=" CA PHE B 253 " ideal model delta sigma weight residual 122.87 128.07 -5.20 1.61e+00 3.86e-01 1.04e+01 angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" C SER A 13 " ideal model delta sigma weight residual 108.13 113.63 -5.50 1.72e+00 3.38e-01 1.02e+01 angle pdb=" CA CYS E 147 " pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " ideal model delta sigma weight residual 114.40 121.55 -7.15 2.30e+00 1.89e-01 9.67e+00 ... (remaining 12074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4825 17.53 - 35.06: 398 35.06 - 52.60: 59 52.60 - 70.13: 5 70.13 - 87.66: 3 Dihedral angle restraints: 5290 sinusoidal: 2086 harmonic: 3204 Sorted by residual: dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 130.87 -37.87 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N CYS B 204 " pdb=" CA CYS B 204 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 692 0.029 - 0.058: 404 0.058 - 0.088: 167 0.088 - 0.117: 84 0.117 - 0.146: 26 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ASN B 237 " pdb=" N ASN B 237 " pdb=" C ASN B 237 " pdb=" CB ASN B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" C PRO G 49 " pdb=" CB PRO G 49 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1370 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 680 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO R 681 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 681 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 681 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 712 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C VAL R 712 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL R 712 " 0.012 2.00e-02 2.50e+03 pdb=" N THR R 713 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 726 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO R 727 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 727 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 727 " -0.025 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 501 2.73 - 3.27: 8190 3.27 - 3.81: 12943 3.81 - 4.36: 15016 4.36 - 4.90: 26925 Nonbonded interactions: 63575 Sorted by model distance: nonbonded pdb=" OD2 ASP B 298 " pdb=" NZ LYS B 301 " model vdw 2.184 2.520 nonbonded pdb=" N SER R 531 " pdb=" OH TYR R 683 " model vdw 2.262 2.520 nonbonded pdb=" O ASN B 340 " pdb=" NH2 ARG G 62 " model vdw 2.265 2.520 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.270 2.440 nonbonded pdb=" NH2 ARG B 137 " pdb=" O GLU B 172 " model vdw 2.297 2.520 ... (remaining 63570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.006 0.053 8931 Z= 0.396 Angle : 0.732 7.780 12079 Z= 0.417 Chirality : 0.047 0.146 1373 Planarity : 0.005 0.053 1519 Dihedral : 12.733 87.660 3216 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1093 helix: 1.01 (0.28), residues: 362 sheet: -0.05 (0.32), residues: 272 loop : -1.89 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.010 0.002 HIS E 220 PHE 0.024 0.003 PHE R 627 TYR 0.021 0.002 TYR E 178 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.886 Fit side-chains REVERT: A 262 ASP cc_start: 0.6499 (m-30) cc_final: 0.6256 (m-30) REVERT: B 205 ASP cc_start: 0.7186 (t0) cc_final: 0.6881 (t0) REVERT: B 291 ASP cc_start: 0.6365 (m-30) cc_final: 0.5908 (m-30) REVERT: E 211 ASP cc_start: 0.7345 (m-30) cc_final: 0.7143 (m-30) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2873 time to fit residues: 60.8182 Evaluate side-chains 154 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 75 GLN B 340 ASN E 159 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN R 620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8931 Z= 0.220 Angle : 0.572 7.379 12079 Z= 0.309 Chirality : 0.043 0.151 1373 Planarity : 0.004 0.052 1519 Dihedral : 4.840 21.544 1202 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.57 % Allowed : 6.37 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.09 (0.26), residues: 1093 helix: 1.85 (0.28), residues: 366 sheet: 0.17 (0.32), residues: 279 loop : -1.90 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS E 220 PHE 0.025 0.002 PHE A 273 TYR 0.017 0.002 TYR B 105 ARG 0.001 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 1.031 Fit side-chains REVERT: A 33 GLU cc_start: 0.6971 (tt0) cc_final: 0.6746 (tt0) REVERT: A 212 PHE cc_start: 0.8016 (p90) cc_final: 0.7590 (p90) REVERT: A 262 ASP cc_start: 0.6431 (m-30) cc_final: 0.6178 (m-30) REVERT: B 61 MET cc_start: 0.8303 (ppp) cc_final: 0.7887 (ppp) REVERT: R 721 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7282 (mmmm) outliers start: 15 outliers final: 7 residues processed: 180 average time/residue: 0.2911 time to fit residues: 66.2000 Evaluate side-chains 171 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8931 Z= 0.166 Angle : 0.524 7.966 12079 Z= 0.280 Chirality : 0.042 0.151 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.496 20.252 1202 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.57 % Allowed : 10.03 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.25 (0.26), residues: 1093 helix: 2.30 (0.28), residues: 367 sheet: 0.30 (0.32), residues: 272 loop : -1.80 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 220 PHE 0.018 0.001 PHE A 273 TYR 0.011 0.001 TYR B 105 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.050 Fit side-chains REVERT: A 212 PHE cc_start: 0.7987 (p90) cc_final: 0.7593 (p90) REVERT: A 262 ASP cc_start: 0.6367 (m-30) cc_final: 0.6118 (m-30) REVERT: B 19 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7696 (ttp-170) REVERT: R 761 ASP cc_start: 0.5659 (m-30) cc_final: 0.5175 (t0) outliers start: 15 outliers final: 8 residues processed: 178 average time/residue: 0.2930 time to fit residues: 66.7968 Evaluate side-chains 169 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8931 Z= 0.236 Angle : 0.566 8.047 12079 Z= 0.299 Chirality : 0.042 0.141 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.566 22.159 1202 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.46 % Allowed : 11.91 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1093 helix: 2.31 (0.28), residues: 367 sheet: 0.34 (0.32), residues: 269 loop : -1.80 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS E 220 PHE 0.015 0.002 PHE E 200 TYR 0.014 0.002 TYR E 178 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 0.976 Fit side-chains REVERT: A 212 PHE cc_start: 0.8050 (p90) cc_final: 0.7641 (p90) REVERT: A 262 ASP cc_start: 0.6387 (m-30) cc_final: 0.6164 (m-30) REVERT: E 6 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: R 761 ASP cc_start: 0.5713 (m-30) cc_final: 0.5075 (t0) outliers start: 14 outliers final: 11 residues processed: 173 average time/residue: 0.2739 time to fit residues: 61.3411 Evaluate side-chains 174 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8931 Z= 0.224 Angle : 0.551 7.727 12079 Z= 0.293 Chirality : 0.042 0.142 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.517 21.288 1202 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.30 % Allowed : 12.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.40 (0.26), residues: 1093 helix: 2.51 (0.28), residues: 361 sheet: 0.36 (0.32), residues: 270 loop : -1.73 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 220 PHE 0.016 0.002 PHE E 200 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 0.950 Fit side-chains REVERT: A 212 PHE cc_start: 0.8046 (p90) cc_final: 0.7646 (p90) REVERT: A 252 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6887 (t70) REVERT: A 262 ASP cc_start: 0.6367 (m-30) cc_final: 0.6147 (m-30) REVERT: B 19 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7687 (ttp-170) REVERT: R 761 ASP cc_start: 0.5986 (m-30) cc_final: 0.5264 (t0) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.2771 time to fit residues: 59.8995 Evaluate side-chains 177 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 705 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8931 Z= 0.189 Angle : 0.532 8.538 12079 Z= 0.282 Chirality : 0.041 0.140 1373 Planarity : 0.003 0.049 1519 Dihedral : 4.380 20.624 1202 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.09 % Allowed : 14.21 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.50 (0.26), residues: 1093 helix: 2.62 (0.28), residues: 361 sheet: 0.39 (0.32), residues: 272 loop : -1.68 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 220 PHE 0.015 0.001 PHE E 200 TYR 0.010 0.001 TYR R 638 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.021 Fit side-chains REVERT: A 212 PHE cc_start: 0.8044 (p90) cc_final: 0.7639 (p90) REVERT: A 252 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6828 (t70) REVERT: A 262 ASP cc_start: 0.6350 (m-30) cc_final: 0.6133 (m-30) REVERT: B 19 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7692 (ttp-170) REVERT: E 164 TRP cc_start: 0.8233 (m100) cc_final: 0.7584 (m100) REVERT: R 687 ASP cc_start: 0.7896 (t0) cc_final: 0.7653 (m-30) REVERT: R 761 ASP cc_start: 0.5967 (m-30) cc_final: 0.5274 (t0) outliers start: 20 outliers final: 15 residues processed: 172 average time/residue: 0.2779 time to fit residues: 61.1597 Evaluate side-chains 175 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8931 Z= 0.233 Angle : 0.571 9.205 12079 Z= 0.301 Chirality : 0.042 0.141 1373 Planarity : 0.003 0.049 1519 Dihedral : 4.472 22.026 1202 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.88 % Allowed : 15.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.26), residues: 1093 helix: 2.59 (0.28), residues: 361 sheet: 0.42 (0.32), residues: 271 loop : -1.70 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS E 220 PHE 0.029 0.002 PHE A 273 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 0.996 Fit side-chains REVERT: A 212 PHE cc_start: 0.8102 (p90) cc_final: 0.7647 (p90) REVERT: A 252 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6851 (t70) REVERT: A 262 ASP cc_start: 0.6362 (m-30) cc_final: 0.6143 (m-30) REVERT: B 19 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7697 (ttp-170) REVERT: B 205 ASP cc_start: 0.7211 (t0) cc_final: 0.6854 (t0) REVERT: E 164 TRP cc_start: 0.8231 (m100) cc_final: 0.7574 (m100) REVERT: R 687 ASP cc_start: 0.7912 (t0) cc_final: 0.7666 (m-30) REVERT: R 761 ASP cc_start: 0.6017 (m-30) cc_final: 0.5375 (t0) outliers start: 18 outliers final: 16 residues processed: 170 average time/residue: 0.2873 time to fit residues: 62.5217 Evaluate side-chains 180 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.0670 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8931 Z= 0.197 Angle : 0.555 8.354 12079 Z= 0.293 Chirality : 0.041 0.140 1373 Planarity : 0.003 0.048 1519 Dihedral : 4.372 20.669 1202 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.40 % Allowed : 15.26 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.26), residues: 1093 helix: 2.67 (0.28), residues: 362 sheet: 0.44 (0.32), residues: 272 loop : -1.64 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 220 PHE 0.027 0.002 PHE A 273 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8078 (p90) cc_final: 0.7650 (p90) REVERT: A 252 ASP cc_start: 0.7065 (t70) cc_final: 0.6802 (t70) REVERT: A 262 ASP cc_start: 0.6341 (m-30) cc_final: 0.6127 (m-30) REVERT: B 19 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: E 98 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7422 (ptt180) REVERT: E 164 TRP cc_start: 0.8327 (m100) cc_final: 0.7664 (m100) REVERT: R 687 ASP cc_start: 0.7914 (t0) cc_final: 0.7672 (m-30) outliers start: 23 outliers final: 20 residues processed: 172 average time/residue: 0.2955 time to fit residues: 64.5527 Evaluate side-chains 185 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 678 TYR Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 721 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 100 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8931 Z= 0.157 Angle : 0.536 8.421 12079 Z= 0.281 Chirality : 0.040 0.136 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.179 19.178 1202 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.19 % Allowed : 15.67 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.68 (0.26), residues: 1093 helix: 2.79 (0.28), residues: 363 sheet: 0.47 (0.32), residues: 274 loop : -1.60 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.024 0.001 PHE A 273 TYR 0.009 0.001 TYR E 178 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8033 (p90) cc_final: 0.7640 (p90) REVERT: A 262 ASP cc_start: 0.6319 (m-30) cc_final: 0.6104 (m-30) REVERT: B 19 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7688 (ttp-170) REVERT: E 164 TRP cc_start: 0.8324 (m100) cc_final: 0.7663 (m100) REVERT: R 687 ASP cc_start: 0.7840 (t0) cc_final: 0.7603 (m-30) outliers start: 21 outliers final: 18 residues processed: 174 average time/residue: 0.3046 time to fit residues: 67.2368 Evaluate side-chains 182 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 678 TYR Chi-restraints excluded: chain R residue 695 SER Chi-restraints excluded: chain R residue 721 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.2980 chunk 71 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8931 Z= 0.224 Angle : 0.587 9.847 12079 Z= 0.306 Chirality : 0.042 0.141 1373 Planarity : 0.004 0.050 1519 Dihedral : 4.340 21.888 1202 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.67 % Allowed : 16.41 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1093 helix: 2.71 (0.28), residues: 362 sheet: 0.44 (0.32), residues: 274 loop : -1.60 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS E 220 PHE 0.037 0.002 PHE E 227 TYR 0.010 0.001 TYR E 102 ARG 0.003 0.000 ARG E 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8079 (p90) cc_final: 0.7632 (p90) REVERT: A 262 ASP cc_start: 0.6347 (m-30) cc_final: 0.6130 (m-30) REVERT: B 19 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7686 (ttp-170) REVERT: B 205 ASP cc_start: 0.7187 (t0) cc_final: 0.6929 (t0) REVERT: B 219 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7266 (mtt90) REVERT: R 687 ASP cc_start: 0.7944 (t0) cc_final: 0.7712 (m-30) outliers start: 16 outliers final: 15 residues processed: 171 average time/residue: 0.2904 time to fit residues: 63.2117 Evaluate side-chains 181 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain R residue 678 TYR Chi-restraints excluded: chain R residue 695 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120290 restraints weight = 12839.634| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.60 r_work: 0.3465 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8931 Z= 0.225 Angle : 0.594 10.553 12079 Z= 0.309 Chirality : 0.042 0.140 1373 Planarity : 0.003 0.050 1519 Dihedral : 4.370 21.021 1202 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.57 % Allowed : 16.93 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.58 (0.26), residues: 1093 helix: 2.65 (0.27), residues: 362 sheet: 0.40 (0.32), residues: 270 loop : -1.58 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 332 HIS 0.005 0.001 HIS E 220 PHE 0.036 0.002 PHE E 227 TYR 0.011 0.001 TYR R 638 ARG 0.002 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.66 seconds wall clock time: 42 minutes 23.90 seconds (2543.90 seconds total)