Starting phenix.real_space_refine on Wed Feb 4 13:43:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klv_62417/02_2026/9klv_62417.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 72 5.16 5 C 6772 2.51 5 N 1872 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10732 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 16, 'TRANS': 321} Chain breaks: 3 Chain: "B" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1045 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Chain: "A" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2094 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 15, 'TRANS': 253} Chain: "C" Number of atoms: 5007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5007 Classifications: {'peptide': 641} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 608} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'GR2': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GR2:plan-1': 1, 'GR2:plan-2': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.01, per 1000 atoms: 0.19 Number of scatterers: 10732 At special positions: 0 Unit cell: (89.06, 124.83, 127.02, 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 72 16.00 O 2016 8.00 N 1872 7.00 C 6772 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 402.1 milliseconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 51.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'D' and resid 13 through 31 removed outlier: 3.662A pdb=" N ARG D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.857A pdb=" N VAL D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 4.474A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 60 " --> pdb=" O CYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 65 through 82 removed outlier: 4.182A pdb=" N CYS D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 115 removed outlier: 4.158A pdb=" N CYS D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 140 through 150 removed outlier: 3.599A pdb=" N GLU D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 150 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 removed outlier: 3.522A pdb=" N ASN D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 620 removed outlier: 4.880A pdb=" N GLY D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 640 Processing helix chain 'D' and resid 661 through 677 Processing helix chain 'D' and resid 696 through 700 Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 725 through 728 removed outlier: 3.530A pdb=" N ALA D 728 " --> pdb=" O ILE D 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 725 through 728' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 862 through 866 Processing helix chain 'D' and resid 867 through 869 No H-bonds generated for 'chain 'D' and resid 867 through 869' Processing helix chain 'D' and resid 870 through 877 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.799A pdb=" N SER B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 48 through 64 removed outlier: 3.595A pdb=" N LEU B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.903A pdb=" N MET B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.603A pdb=" N SER A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.142A pdb=" N TYR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.842A pdb=" N ALA A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.527A pdb=" N MET A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.621A pdb=" N PHE A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 198 through 205 removed outlier: 4.005A pdb=" N GLY A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 4.095A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 252 through 266 Proline residue: A 258 - end of helix Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.611A pdb=" N LEU C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 121 through 132 removed outlier: 4.305A pdb=" N GLY C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.639A pdb=" N ILE C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 202 through 209 removed outlier: 3.506A pdb=" N ALA C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 removed outlier: 3.569A pdb=" N LEU C 218 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 288 through 291 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.123A pdb=" N PHE C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.585A pdb=" N ASN C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.734A pdb=" N GLY C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.594A pdb=" N TYR C 590 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.827A pdb=" N TRP C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 681 through 685 Processing helix chain 'C' and resid 710 through 724 Processing sheet with id=AA1, first strand: chain 'D' and resid 682 through 685 removed outlier: 6.193A pdb=" N ILE D 682 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU D 723 " --> pdb=" O ILE D 682 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE D 684 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 654 " --> pdb=" O ASP D 879 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL D 881 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 656 " --> pdb=" O VAL D 881 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 744 through 746 Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.555A pdb=" N VAL A 20 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR A 49 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 22 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS A 89 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL A 116 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A 91 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N HIS A 210 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 115 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 212 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET A 117 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N SER A 214 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 80 removed outlier: 5.191A pdb=" N SER C 195 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG C 165 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 197 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS C 335 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 330 " --> pdb=" O LYS C 359 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY C 361 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU C 332 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE C 363 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N LEU C 334 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 386 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N TYR C 415 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 388 " --> pdb=" O TYR C 415 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 469 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 466 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TRP C 539 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 468 " --> pdb=" O TRP C 539 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N PHE C 541 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY C 601 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY C 569 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 603 " --> pdb=" O GLY C 569 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1806 1.31 - 1.44: 2728 1.44 - 1.56: 6294 1.56 - 1.69: 0 1.69 - 1.82: 108 Bond restraints: 10936 Sorted by residual: bond pdb=" C14 GR2 A 301 " pdb=" C15 GR2 A 301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C16 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.350 1.417 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C13 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" C15 GR2 A 301 " pdb=" C17 GR2 A 301 " ideal model delta sigma weight residual 1.482 1.525 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" CB MET D 683 " pdb=" CG MET D 683 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 ... (remaining 10931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 14593 2.43 - 4.85: 202 4.85 - 7.28: 22 7.28 - 9.71: 1 9.71 - 12.13: 1 Bond angle restraints: 14819 Sorted by residual: angle pdb=" CB MET D 683 " pdb=" CG MET D 683 " pdb=" SD MET D 683 " ideal model delta sigma weight residual 112.70 124.83 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA GLU D 73 " pdb=" CB GLU D 73 " pdb=" CG GLU D 73 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.69e+00 angle pdb=" CA MET C 49 " pdb=" CB MET C 49 " pdb=" CG MET C 49 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.20e+00 angle pdb=" C PHE B 137 " pdb=" N ASN B 138 " pdb=" CA ASN B 138 " ideal model delta sigma weight residual 122.46 126.49 -4.03 1.41e+00 5.03e-01 8.15e+00 angle pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " pdb=" CG ASN B 109 " ideal model delta sigma weight residual 112.60 115.44 -2.84 1.00e+00 1.00e+00 8.07e+00 ... (remaining 14814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5994 17.93 - 35.86: 510 35.86 - 53.79: 134 53.79 - 71.72: 15 71.72 - 89.65: 17 Dihedral angle restraints: 6670 sinusoidal: 2674 harmonic: 3996 Sorted by residual: dihedral pdb=" CA MET C 596 " pdb=" C MET C 596 " pdb=" N HIS C 597 " pdb=" CA HIS C 597 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU C 621 " pdb=" CG GLU C 621 " pdb=" CD GLU C 621 " pdb=" OE1 GLU C 621 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ILE D 137 " pdb=" C ILE D 137 " pdb=" N LEU D 138 " pdb=" CA LEU D 138 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1090 0.037 - 0.074: 431 0.074 - 0.111: 154 0.111 - 0.148: 28 0.148 - 0.185: 2 Chirality restraints: 1705 Sorted by residual: chirality pdb=" CB ILE D 135 " pdb=" CA ILE D 135 " pdb=" CG1 ILE D 135 " pdb=" CG2 ILE D 135 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CB VAL D 19 " pdb=" CA VAL D 19 " pdb=" CG1 VAL D 19 " pdb=" CG2 VAL D 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CG LEU C 40 " pdb=" CB LEU C 40 " pdb=" CD1 LEU C 40 " pdb=" CD2 LEU C 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 1702 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 109 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASN B 109 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN B 109 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE B 110 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 82 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C ARG D 82 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG D 82 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU D 83 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 342 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO C 343 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.021 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1362 2.75 - 3.28: 10896 3.28 - 3.82: 18060 3.82 - 4.36: 21567 4.36 - 4.90: 36636 Nonbonded interactions: 88521 Sorted by model distance: nonbonded pdb=" OH TYR A 67 " pdb=" OD2 ASP A 76 " model vdw 2.207 3.040 nonbonded pdb=" N ASP C 202 " pdb=" OD1 ASP C 202 " model vdw 2.243 3.120 nonbonded pdb=" O HIS D 60 " pdb=" OG SER D 63 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP D 741 " pdb=" NH1 ARG D 876 " model vdw 2.258 3.120 nonbonded pdb=" CA GLY D 651 " pdb=" OD1 ASN D 757 " model vdw 2.281 3.440 ... (remaining 88516 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 ========== 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: 2.910 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.110 10937 Z= 0.232 Angle : 0.703 12.134 14819 Z= 0.366 Chirality : 0.044 0.185 1705 Planarity : 0.005 0.052 1909 Dihedral : 14.939 89.655 4072 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.35 % Allowed : 16.34 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1358 helix: 0.69 (0.21), residues: 617 sheet: -0.47 (0.38), residues: 207 loop : 0.03 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 152 TYR 0.014 0.002 TYR C 260 PHE 0.024 0.002 PHE D 717 TRP 0.024 0.002 TRP D 766 HIS 0.005 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00519 (10936) covalent geometry : angle 0.70348 (14819) hydrogen bonds : bond 0.17335 ( 486) hydrogen bonds : angle 6.26820 ( 1359) Misc. bond : bond 0.01063 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: D 53 ARG cc_start: 0.8942 (ttt180) cc_final: 0.8659 (mmt180) REVERT: D 98 ASN cc_start: 0.8582 (m-40) cc_final: 0.8197 (t0) REVERT: D 105 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8357 (ptmt) REVERT: D 616 MET cc_start: 0.6074 (mtm) cc_final: 0.5423 (ptp) REVERT: D 729 ASP cc_start: 0.8373 (m-30) cc_final: 0.8160 (p0) REVERT: B 16 PHE cc_start: 0.6854 (m-80) cc_final: 0.6510 (m-80) REVERT: B 27 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 51 ILE cc_start: 0.8692 (mm) cc_final: 0.8489 (mm) REVERT: B 94 ASP cc_start: 0.8175 (t0) cc_final: 0.7817 (p0) REVERT: B 108 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 135 THR cc_start: 0.9238 (m) cc_final: 0.8923 (p) REVERT: A 147 ASP cc_start: 0.9097 (t0) cc_final: 0.8754 (m-30) REVERT: A 151 LYS cc_start: 0.8908 (tppp) cc_final: 0.8691 (ttmm) REVERT: A 180 ASN cc_start: 0.8852 (t0) cc_final: 0.8121 (t0) REVERT: C 39 ASP cc_start: 0.8577 (m-30) cc_final: 0.8164 (t0) REVERT: C 160 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8248 (mtm110) REVERT: C 438 ASP cc_start: 0.8429 (t0) cc_final: 0.8185 (t0) REVERT: C 705 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: C 723 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.8189 (mtm110) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.0999 time to fit residues: 21.8751 Evaluate side-chains 131 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071643 restraints weight = 22570.752| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.62 r_work: 0.2831 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10937 Z= 0.112 Angle : 0.564 8.225 14819 Z= 0.285 Chirality : 0.042 0.176 1705 Planarity : 0.004 0.040 1909 Dihedral : 5.139 51.264 1510 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.29 % Allowed : 14.15 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1358 helix: 1.08 (0.22), residues: 611 sheet: -0.45 (0.38), residues: 207 loop : 0.22 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 876 TYR 0.009 0.001 TYR A 201 PHE 0.018 0.001 PHE D 717 TRP 0.025 0.001 TRP D 766 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00241 (10936) covalent geometry : angle 0.56439 (14819) hydrogen bonds : bond 0.03589 ( 486) hydrogen bonds : angle 4.70294 ( 1359) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8515 (mt0) REVERT: D 53 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8655 (mmt180) REVERT: D 98 ASN cc_start: 0.8673 (m-40) cc_final: 0.8093 (t0) REVERT: D 105 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8356 (ptmt) REVERT: D 115 CYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5559 (t) REVERT: D 616 MET cc_start: 0.6009 (mtm) cc_final: 0.5793 (ptm) REVERT: D 648 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7895 (mm) REVERT: B 16 PHE cc_start: 0.6779 (m-80) cc_final: 0.6422 (m-80) REVERT: B 27 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 108 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 135 THR cc_start: 0.9213 (m) cc_final: 0.8889 (p) REVERT: B 143 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: A 180 ASN cc_start: 0.8811 (t0) cc_final: 0.8029 (t0) REVERT: C 49 MET cc_start: 0.9020 (ttp) cc_final: 0.8258 (ttt) REVERT: C 70 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9069 (mp) REVERT: C 111 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8681 (t70) REVERT: C 160 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8213 (mtp85) outliers start: 39 outliers final: 13 residues processed: 171 average time/residue: 0.0915 time to fit residues: 22.3082 Evaluate side-chains 134 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.069707 restraints weight = 22622.511| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.67 r_work: 0.2780 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10937 Z= 0.115 Angle : 0.543 13.224 14819 Z= 0.269 Chirality : 0.041 0.220 1705 Planarity : 0.004 0.043 1909 Dihedral : 4.573 52.105 1496 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.12 % Allowed : 15.33 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1358 helix: 1.21 (0.22), residues: 613 sheet: -0.59 (0.37), residues: 207 loop : 0.26 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 876 TYR 0.006 0.001 TYR B 58 PHE 0.012 0.001 PHE D 717 TRP 0.018 0.001 TRP D 766 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00260 (10936) covalent geometry : angle 0.54289 (14819) hydrogen bonds : bond 0.03402 ( 486) hydrogen bonds : angle 4.46812 ( 1359) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8497 (mt0) REVERT: D 53 ARG cc_start: 0.8904 (ttt180) cc_final: 0.8635 (tpt90) REVERT: D 98 ASN cc_start: 0.8648 (m-40) cc_final: 0.8062 (t0) REVERT: D 105 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8300 (ptmt) REVERT: D 115 CYS cc_start: 0.6434 (OUTLIER) cc_final: 0.5428 (t) REVERT: D 612 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5148 (pt) REVERT: D 616 MET cc_start: 0.6113 (mtm) cc_final: 0.5764 (ptp) REVERT: D 766 TRP cc_start: 0.7353 (m-90) cc_final: 0.7115 (m-90) REVERT: B 27 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 108 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 135 THR cc_start: 0.9184 (m) cc_final: 0.8835 (p) REVERT: B 143 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: C 39 ASP cc_start: 0.8508 (m-30) cc_final: 0.8162 (t0) REVERT: C 49 MET cc_start: 0.8970 (ttp) cc_final: 0.8276 (ttt) REVERT: C 70 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8955 (mp) REVERT: C 111 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8561 (t70) REVERT: C 160 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7906 (mtp85) REVERT: C 596 MET cc_start: 0.8804 (tpp) cc_final: 0.8548 (ttm) REVERT: C 684 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8310 (mtp180) REVERT: C 705 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7832 (tmm) outliers start: 37 outliers final: 16 residues processed: 159 average time/residue: 0.1031 time to fit residues: 22.6808 Evaluate side-chains 143 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS C 168 GLN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.064300 restraints weight = 23292.006| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.64 r_work: 0.2663 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 10937 Z= 0.332 Angle : 0.708 8.391 14819 Z= 0.355 Chirality : 0.048 0.154 1705 Planarity : 0.005 0.054 1909 Dihedral : 5.421 55.062 1496 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.30 % Allowed : 15.16 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1358 helix: 0.58 (0.21), residues: 626 sheet: -0.77 (0.36), residues: 208 loop : -0.09 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 876 TYR 0.014 0.002 TYR C 260 PHE 0.018 0.002 PHE C 582 TRP 0.011 0.002 TRP C 639 HIS 0.008 0.002 HIS D 749 Details of bonding type rmsd covalent geometry : bond 0.00765 (10936) covalent geometry : angle 0.70790 (14819) hydrogen bonds : bond 0.04637 ( 486) hydrogen bonds : angle 4.79554 ( 1359) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7765 (p) REVERT: D 53 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8642 (mmt180) REVERT: D 98 ASN cc_start: 0.8713 (m-40) cc_final: 0.8133 (t0) REVERT: D 105 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8525 (ptmt) REVERT: D 115 CYS cc_start: 0.6570 (OUTLIER) cc_final: 0.5601 (t) REVERT: D 667 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8419 (tttp) REVERT: D 766 TRP cc_start: 0.7447 (m-90) cc_final: 0.7156 (m-90) REVERT: D 871 HIS cc_start: 0.7672 (m170) cc_final: 0.7166 (m90) REVERT: B 27 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 108 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 135 THR cc_start: 0.9286 (m) cc_final: 0.8940 (p) REVERT: C 111 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (t70) REVERT: C 160 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8252 (mtm110) REVERT: C 534 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8675 (mtm-85) REVERT: C 568 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: C 684 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8367 (ttp-170) REVERT: C 705 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8198 (tmm) outliers start: 51 outliers final: 25 residues processed: 163 average time/residue: 0.1047 time to fit residues: 23.5268 Evaluate side-chains 146 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067402 restraints weight = 22842.882| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.57 r_work: 0.2729 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10937 Z= 0.143 Angle : 0.566 7.737 14819 Z= 0.281 Chirality : 0.042 0.159 1705 Planarity : 0.004 0.039 1909 Dihedral : 5.010 54.880 1496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.12 % Allowed : 16.51 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1358 helix: 0.78 (0.21), residues: 628 sheet: -0.77 (0.36), residues: 207 loop : -0.01 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 876 TYR 0.011 0.001 TYR C 624 PHE 0.011 0.001 PHE C 623 TRP 0.010 0.001 TRP D 654 HIS 0.007 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00331 (10936) covalent geometry : angle 0.56601 (14819) hydrogen bonds : bond 0.03508 ( 486) hydrogen bonds : angle 4.52415 ( 1359) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 ARG cc_start: 0.8982 (ttt180) cc_final: 0.8652 (ttt90) REVERT: D 98 ASN cc_start: 0.8703 (m-40) cc_final: 0.8109 (t0) REVERT: D 105 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8499 (ptmt) REVERT: D 115 CYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5713 (t) REVERT: D 667 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8444 (tttp) REVERT: D 871 HIS cc_start: 0.7686 (m170) cc_final: 0.7169 (m90) REVERT: B 27 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 108 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 135 THR cc_start: 0.9280 (m) cc_final: 0.8927 (p) REVERT: C 49 MET cc_start: 0.9043 (ttp) cc_final: 0.8773 (ttt) REVERT: C 90 MET cc_start: 0.8631 (mpp) cc_final: 0.8429 (mpp) REVERT: C 111 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8693 (t70) REVERT: C 160 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8066 (mtp85) REVERT: C 294 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8424 (mtt180) REVERT: C 534 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8517 (mtm-85) REVERT: C 568 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: C 684 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8380 (ttt-90) REVERT: C 705 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8279 (tmm) outliers start: 37 outliers final: 17 residues processed: 162 average time/residue: 0.1011 time to fit residues: 22.7710 Evaluate side-chains 142 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 0.0050 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.068477 restraints weight = 22835.825| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.03 r_work: 0.2698 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10937 Z= 0.136 Angle : 0.569 13.346 14819 Z= 0.279 Chirality : 0.044 0.656 1705 Planarity : 0.004 0.040 1909 Dihedral : 4.814 57.998 1494 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.78 % Allowed : 16.76 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1358 helix: 1.00 (0.22), residues: 621 sheet: -0.79 (0.36), residues: 208 loop : 0.07 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 148 TYR 0.009 0.001 TYR C 624 PHE 0.013 0.001 PHE D 717 TRP 0.049 0.001 TRP D 654 HIS 0.008 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00315 (10936) covalent geometry : angle 0.56894 (14819) hydrogen bonds : bond 0.03268 ( 486) hydrogen bonds : angle 4.43082 ( 1359) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8453 (mt0) REVERT: D 53 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8642 (ttt90) REVERT: D 98 ASN cc_start: 0.8695 (m-40) cc_final: 0.8077 (t0) REVERT: D 105 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8462 (ptmt) REVERT: D 115 CYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5544 (t) REVERT: D 139 ASP cc_start: 0.8224 (t0) cc_final: 0.8012 (t0) REVERT: D 616 MET cc_start: 0.5572 (ptp) cc_final: 0.4833 (ptp) REVERT: D 667 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8457 (tttp) REVERT: D 766 TRP cc_start: 0.7432 (m-90) cc_final: 0.7097 (m-90) REVERT: D 871 HIS cc_start: 0.7678 (m170) cc_final: 0.7191 (m90) REVERT: B 27 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 108 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 135 THR cc_start: 0.9281 (m) cc_final: 0.8941 (p) REVERT: C 49 MET cc_start: 0.8981 (ttp) cc_final: 0.8471 (ttt) REVERT: C 90 MET cc_start: 0.8510 (mpp) cc_final: 0.8293 (mpp) REVERT: C 111 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8573 (t70) REVERT: C 160 ARG cc_start: 0.8311 (mtp85) cc_final: 0.8025 (mtm110) REVERT: C 534 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8350 (mtm-85) REVERT: C 568 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: C 684 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8178 (ttt-90) REVERT: C 705 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8115 (tmm) outliers start: 33 outliers final: 20 residues processed: 164 average time/residue: 0.1030 time to fit residues: 23.4991 Evaluate side-chains 152 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 0.0470 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.067478 restraints weight = 22899.320| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.05 r_work: 0.2690 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10937 Z= 0.156 Angle : 0.569 8.282 14819 Z= 0.281 Chirality : 0.042 0.153 1705 Planarity : 0.004 0.039 1909 Dihedral : 4.844 59.652 1494 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.29 % Allowed : 17.02 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1358 helix: 0.97 (0.22), residues: 630 sheet: -0.83 (0.36), residues: 208 loop : 0.07 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 148 TYR 0.009 0.001 TYR C 624 PHE 0.015 0.001 PHE D 717 TRP 0.032 0.001 TRP D 654 HIS 0.006 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00367 (10936) covalent geometry : angle 0.56860 (14819) hydrogen bonds : bond 0.03348 ( 486) hydrogen bonds : angle 4.40565 ( 1359) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.8519 (pp) cc_final: 0.8200 (tp) REVERT: D 22 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8449 (mt0) REVERT: D 53 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8634 (ttt90) REVERT: D 98 ASN cc_start: 0.8687 (m-40) cc_final: 0.7993 (t0) REVERT: D 101 MET cc_start: 0.8411 (mpp) cc_final: 0.8188 (mpp) REVERT: D 105 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8455 (ptmt) REVERT: D 115 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5597 (t) REVERT: D 139 ASP cc_start: 0.8299 (t0) cc_final: 0.8091 (t0) REVERT: D 162 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5973 (mt-10) REVERT: D 667 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8453 (tttp) REVERT: D 871 HIS cc_start: 0.7699 (m170) cc_final: 0.7226 (m90) REVERT: B 108 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 135 THR cc_start: 0.9292 (m) cc_final: 0.8955 (p) REVERT: A 180 ASN cc_start: 0.8792 (t0) cc_final: 0.7950 (t0) REVERT: C 49 MET cc_start: 0.9005 (ttp) cc_final: 0.8528 (ttt) REVERT: C 111 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8561 (t70) REVERT: C 160 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7977 (mtp85) REVERT: C 294 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (mtt180) REVERT: C 534 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8340 (mtm-85) REVERT: C 568 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: C 684 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (ttt-90) REVERT: C 705 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8096 (tmm) outliers start: 39 outliers final: 22 residues processed: 168 average time/residue: 0.0900 time to fit residues: 21.3216 Evaluate side-chains 158 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.069628 restraints weight = 22819.971| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.99 r_work: 0.2725 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10937 Z= 0.104 Angle : 0.540 9.686 14819 Z= 0.267 Chirality : 0.041 0.169 1705 Planarity : 0.004 0.040 1909 Dihedral : 4.640 58.983 1494 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.61 % Allowed : 17.69 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1358 helix: 1.11 (0.22), residues: 621 sheet: -0.85 (0.35), residues: 208 loop : 0.17 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 148 TYR 0.008 0.001 TYR C 624 PHE 0.016 0.001 PHE D 717 TRP 0.027 0.001 TRP D 654 HIS 0.007 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00237 (10936) covalent geometry : angle 0.53982 (14819) hydrogen bonds : bond 0.02943 ( 486) hydrogen bonds : angle 4.30507 ( 1359) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.8551 (pp) cc_final: 0.8256 (tp) REVERT: D 22 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8418 (mt0) REVERT: D 53 ARG cc_start: 0.8934 (ttt180) cc_final: 0.8613 (ttt90) REVERT: D 98 ASN cc_start: 0.8692 (m-40) cc_final: 0.8076 (t0) REVERT: D 105 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8409 (ptmt) REVERT: D 115 CYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5626 (t) REVERT: D 131 GLU cc_start: 0.8893 (pm20) cc_final: 0.8419 (pm20) REVERT: D 139 ASP cc_start: 0.8329 (t0) cc_final: 0.8099 (t0) REVERT: D 162 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5767 (mt-10) REVERT: D 667 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8440 (tttp) REVERT: D 766 TRP cc_start: 0.7306 (m-90) cc_final: 0.6949 (m-90) REVERT: D 871 HIS cc_start: 0.7660 (m170) cc_final: 0.7194 (m90) REVERT: B 108 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 109 ASN cc_start: 0.8475 (t0) cc_final: 0.8144 (t0) REVERT: B 128 LYS cc_start: 0.8858 (mttp) cc_final: 0.8438 (mttp) REVERT: B 135 THR cc_start: 0.9294 (m) cc_final: 0.8955 (p) REVERT: B 143 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: A 45 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8870 (tttm) REVERT: A 180 ASN cc_start: 0.8798 (t0) cc_final: 0.7934 (t0) REVERT: C 49 MET cc_start: 0.8910 (ttp) cc_final: 0.8495 (ttt) REVERT: C 102 ASP cc_start: 0.8458 (t0) cc_final: 0.8235 (t0) REVERT: C 111 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (t70) REVERT: C 160 ARG cc_start: 0.8278 (mtp85) cc_final: 0.8042 (mtm110) REVERT: C 294 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8386 (mtt180) REVERT: C 534 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8302 (mtm-85) REVERT: C 684 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8346 (mtp180) REVERT: C 705 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7858 (tmm) outliers start: 31 outliers final: 15 residues processed: 163 average time/residue: 0.1062 time to fit residues: 24.0795 Evaluate side-chains 157 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 115 CYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0060 chunk 124 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.069713 restraints weight = 22517.519| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.61 r_work: 0.2786 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10937 Z= 0.097 Angle : 0.547 10.629 14819 Z= 0.267 Chirality : 0.041 0.180 1705 Planarity : 0.003 0.041 1909 Dihedral : 4.187 57.701 1492 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.11 % Allowed : 18.45 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1358 helix: 1.18 (0.22), residues: 622 sheet: -0.92 (0.38), residues: 181 loop : 0.31 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 724 TYR 0.005 0.001 TYR C 624 PHE 0.014 0.001 PHE D 717 TRP 0.027 0.001 TRP D 654 HIS 0.009 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00216 (10936) covalent geometry : angle 0.54684 (14819) hydrogen bonds : bond 0.02777 ( 486) hydrogen bonds : angle 4.21260 ( 1359) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.8564 (pp) cc_final: 0.8258 (tp) REVERT: D 22 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8438 (mt0) REVERT: D 53 ARG cc_start: 0.8980 (ttt180) cc_final: 0.8668 (ttt90) REVERT: D 98 ASN cc_start: 0.8695 (m-40) cc_final: 0.8060 (t0) REVERT: D 105 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8372 (ptmt) REVERT: D 131 GLU cc_start: 0.9072 (pm20) cc_final: 0.8572 (pm20) REVERT: D 137 ILE cc_start: 0.9278 (pt) cc_final: 0.8947 (mm) REVERT: D 139 ASP cc_start: 0.8441 (t0) cc_final: 0.8180 (t0) REVERT: D 162 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5551 (mm-30) REVERT: D 667 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8393 (tttp) REVERT: D 683 MET cc_start: 0.8070 (mmp) cc_final: 0.6801 (ttt) REVERT: D 871 HIS cc_start: 0.7714 (m170) cc_final: 0.7230 (m90) REVERT: B 108 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8066 (tp) REVERT: B 109 ASN cc_start: 0.8496 (t0) cc_final: 0.8137 (t0) REVERT: B 123 ASP cc_start: 0.8581 (m-30) cc_final: 0.8379 (m-30) REVERT: B 128 LYS cc_start: 0.8843 (mttp) cc_final: 0.8412 (mttp) REVERT: B 135 THR cc_start: 0.9308 (m) cc_final: 0.8970 (p) REVERT: B 143 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 45 LYS cc_start: 0.9241 (ttmm) cc_final: 0.8932 (tttm) REVERT: A 180 ASN cc_start: 0.8859 (t0) cc_final: 0.8013 (t0) REVERT: C 102 ASP cc_start: 0.8630 (t0) cc_final: 0.8416 (t0) REVERT: C 111 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8609 (t70) REVERT: C 160 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8189 (mtm110) REVERT: C 534 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8445 (mtm-85) REVERT: C 684 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: C 705 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8016 (tmm) outliers start: 25 outliers final: 13 residues processed: 169 average time/residue: 0.1065 time to fit residues: 24.9839 Evaluate side-chains 158 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070382 restraints weight = 22605.974| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.79 r_work: 0.2764 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.003 0.039 10937 Z= 0.112 Angle : 0.560 12.355 14819 Z= 0.273 Chirality : 0.041 0.174 1705 Planarity : 0.004 0.041 1909 Dihedral : 4.154 58.520 1492 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.94 % Allowed : 18.62 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1358 helix: 1.23 (0.22), residues: 622 sheet: -0.82 (0.37), residues: 199 loop : 0.26 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 61 TYR 0.007 0.001 TYR B 58 PHE 0.015 0.001 PHE D 717 TRP 0.030 0.001 TRP D 654 HIS 0.008 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00261 (10936) covalent geometry : angle 0.56001 (14819) hydrogen bonds : bond 0.02959 ( 486) hydrogen bonds : angle 4.22302 ( 1359) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LEU cc_start: 0.8554 (pp) cc_final: 0.8252 (tp) REVERT: D 22 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8427 (mt0) REVERT: D 53 ARG cc_start: 0.8946 (ttt180) cc_final: 0.8642 (ttt90) REVERT: D 98 ASN cc_start: 0.8624 (m-40) cc_final: 0.7981 (t0) REVERT: D 101 MET cc_start: 0.8284 (mpp) cc_final: 0.8082 (mpp) REVERT: D 105 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8354 (ptmt) REVERT: D 137 ILE cc_start: 0.9264 (pt) cc_final: 0.8988 (mm) REVERT: D 139 ASP cc_start: 0.8326 (t0) cc_final: 0.8064 (t0) REVERT: D 162 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5724 (mt-10) REVERT: D 667 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8388 (tttp) REVERT: D 683 MET cc_start: 0.7858 (mmp) cc_final: 0.6499 (ttt) REVERT: D 871 HIS cc_start: 0.7581 (m170) cc_final: 0.7122 (m90) REVERT: B 91 MET cc_start: 0.8036 (mmm) cc_final: 0.7773 (mmm) REVERT: B 108 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 109 ASN cc_start: 0.8494 (t0) cc_final: 0.8152 (t0) REVERT: B 128 LYS cc_start: 0.8845 (mttp) cc_final: 0.8413 (mttp) REVERT: B 135 THR cc_start: 0.9299 (m) cc_final: 0.8967 (p) REVERT: B 143 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: A 45 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8881 (tttm) REVERT: A 180 ASN cc_start: 0.8820 (t0) cc_final: 0.7926 (t0) REVERT: C 111 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8504 (t70) REVERT: C 160 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7939 (mtp85) REVERT: C 534 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8247 (mtm-85) REVERT: C 684 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: C 705 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7832 (tmm) outliers start: 23 outliers final: 13 residues processed: 158 average time/residue: 0.0980 time to fit residues: 21.9626 Evaluate side-chains 153 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 HIS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 726 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 69 optimal weight: 0.0020 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.070293 restraints weight = 22681.907| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.61 r_work: 0.2795 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10937 Z= 0.096 Angle : 0.552 12.393 14819 Z= 0.270 Chirality : 0.041 0.175 1705 Planarity : 0.003 0.041 1909 Dihedral : 4.048 59.583 1492 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 18.53 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1358 helix: 1.28 (0.22), residues: 621 sheet: -0.83 (0.37), residues: 199 loop : 0.30 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.005 0.001 TYR C 624 PHE 0.014 0.001 PHE D 717 TRP 0.044 0.001 TRP D 654 HIS 0.006 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00214 (10936) covalent geometry : angle 0.55222 (14819) hydrogen bonds : bond 0.02726 ( 486) hydrogen bonds : angle 4.17211 ( 1359) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.63 seconds wall clock time: 46 minutes 28.80 seconds (2788.80 seconds total)