Starting phenix.real_space_refine on Sat Feb 7 18:41:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655.map" model { file = "/net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soe_40655/02_2026/8soe_40655_trim.cif" } resolution = 3.6 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= 0.004 sd= 0.999 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 105 5.16 5 C 11275 2.51 5 N 3094 2.21 5 O 3313 1.98 5 H 17742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 35531 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "A" Number of atoms: 15325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 15325 Classifications: {'peptide': 937} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 891} Chain breaks: 11 Chain: "B" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7919 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 470} Chain breaks: 9 Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "F" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.08, per 1000 atoms: 0.17 Number of scatterers: 35531 At special positions: 0 Unit cell: (99.36, 149.04, 186.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 2 15.00 O 3313 8.00 N 3094 7.00 C 11275 6.00 H 17742 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4250 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 26 sheets defined 38.3% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 2 through 26 removed outlier: 3.915A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'E' and resid 3 through 26 removed outlier: 3.913A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.404A pdb=" N TYR A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.646A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.803A pdb=" N LEU A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.514A pdb=" N LYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.692A pdb=" N MET A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.718A pdb=" N PHE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.524A pdb=" N VAL A 349 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.679A pdb=" N VAL A 604 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 625 through 630 removed outlier: 3.670A pdb=" N GLN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 652 through 668 removed outlier: 5.096A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.736A pdb=" N ARG A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.518A pdb=" N GLY A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 725 through 751 Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 839 through 858 Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 917 through 943 removed outlier: 3.559A pdb=" N CYS A 936 " --> pdb=" O CYS A 932 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.514A pdb=" N LEU A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1021 Processing helix chain 'A' and resid 1023 through 1036 Processing helix chain 'A' and resid 1046 through 1048 No H-bonds generated for 'chain 'A' and resid 1046 through 1048' Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1062 through 1076 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.667A pdb=" N LEU B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 Proline residue: B 52 - end of helix No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 53 through 73 removed outlier: 3.957A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 59 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 removed outlier: 3.671A pdb=" N LEU B 77 " --> pdb=" O THR B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 78 through 90 removed outlier: 3.724A pdb=" N TYR B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 4.016A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 118 through 136 removed outlier: 4.083A pdb=" N GLU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.695A pdb=" N LEU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.722A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.905A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'B' and resid 245 through 261 removed outlier: 3.534A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.621A pdb=" N GLU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 525 No H-bonds generated for 'chain 'B' and resid 524 through 525' Processing helix chain 'B' and resid 527 through 527 No H-bonds generated for 'chain 'B' and resid 527 through 527' Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.977A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 695 through 705 Processing helix chain 'B' and resid 707 through 713 Processing helix chain 'B' and resid 819 through 823 removed outlier: 4.340A pdb=" N ILE B 823 " --> pdb=" O GLU B 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.892A pdb=" N LYS D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 24 Processing helix chain 'F' and resid 29 through 45 Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 59 through 64 removed outlier: 3.904A pdb=" N LYS F 64 " --> pdb=" O PRO F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.028A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.020A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.979A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.712A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.152A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.754A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.719A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 51 removed outlier: 5.813A pdb=" N THR E 47 " --> pdb=" O ASN E 340 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN E 340 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 336 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 63 removed outlier: 3.572A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.943A pdb=" N GLY E 115 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS E 103 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 113 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR E 105 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYR E 111 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY E 116 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.596A pdb=" N CYS E 148 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP E 170 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN E 176 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 187 through 192 removed outlier: 4.240A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 229 through 234 removed outlier: 3.681A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 273 through 278 removed outlier: 3.760A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.704A pdb=" N GLY A 133 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 229 through 236 removed outlier: 4.263A pdb=" N ILE A 303 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.417A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.439A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 392 through 398 removed outlier: 6.660A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 382 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 402 through 403 removed outlier: 3.617A pdb=" N TRP A 485 " --> pdb=" O TYR A 463 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 783 through 784 removed outlier: 4.226A pdb=" N PHE A 783 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 793 " --> pdb=" O PHE A 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 814 through 816 removed outlier: 6.722A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AC6, first strand: chain 'B' and resid 288 through 292 removed outlier: 3.501A pdb=" N LEU B 166 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 161 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL B 518 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 163 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE B 520 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 165 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N MET B 870 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE B 554 " --> pdb=" O MET B 870 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.694A pdb=" N THR B 684 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 676 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE B 828 " --> pdb=" O GLY B 806 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS B 748 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 777 " --> pdb=" O CYS B 748 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 750 " --> pdb=" O THR B 775 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 799 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.694A pdb=" N THR B 684 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 676 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 826 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE B 812 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS B 748 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 777 " --> pdb=" O CYS B 748 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 750 " --> pdb=" O THR B 775 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 799 " --> pdb=" O LEU B 770 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2421 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: 10.48 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17679 1.03 - 1.23: 64 1.23 - 1.42: 7522 1.42 - 1.62: 10472 1.62 - 1.81: 147 Bond restraints: 35884 Sorted by residual: bond pdb=" CA HIS A 199 " pdb=" C HIS A 199 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.38e+00 bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" C TRP A 323 " pdb=" N PRO A 324 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.21e-02 6.83e+03 1.07e+00 bond pdb=" CB PRO B 868 " pdb=" CG PRO B 868 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.58e-01 bond pdb=" CA CYS A 932 " pdb=" C CYS A 932 " ideal model delta sigma weight residual 1.522 1.508 0.013 1.37e-02 5.33e+03 9.27e-01 ... (remaining 35879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 62472 1.34 - 2.68: 2134 2.68 - 4.01: 165 4.01 - 5.35: 30 5.35 - 6.69: 7 Bond angle restraints: 64808 Sorted by residual: angle pdb=" N CYS A 932 " pdb=" CA CYS A 932 " pdb=" C CYS A 932 " ideal model delta sigma weight residual 113.23 108.83 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" C GLU A 852 " pdb=" N SER A 853 " pdb=" CA SER A 853 " ideal model delta sigma weight residual 120.31 114.97 5.34 1.52e+00 4.33e-01 1.24e+01 angle pdb=" N ASN A 430 " pdb=" CA ASN A 430 " pdb=" C ASN A 430 " ideal model delta sigma weight residual 109.24 114.09 -4.85 1.63e+00 3.76e-01 8.86e+00 angle pdb=" N ALA B 532 " pdb=" CA ALA B 532 " pdb=" C ALA B 532 " ideal model delta sigma weight residual 111.36 108.20 3.16 1.09e+00 8.42e-01 8.42e+00 angle pdb=" N ILE B 869 " pdb=" CA ILE B 869 " pdb=" C ILE B 869 " ideal model delta sigma weight residual 110.05 107.04 3.01 1.09e+00 8.42e-01 7.64e+00 ... (remaining 64803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 16109 24.72 - 49.44: 599 49.44 - 74.16: 102 74.16 - 98.88: 14 98.88 - 123.60: 2 Dihedral angle restraints: 16826 sinusoidal: 9188 harmonic: 7638 Sorted by residual: dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 63.60 -123.60 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -174.91 114.90 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA PRO A 590 " pdb=" C PRO A 590 " pdb=" N LYS A 591 " pdb=" CA LYS A 591 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 16823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2059 0.040 - 0.080: 518 0.080 - 0.120: 169 0.120 - 0.160: 47 0.160 - 0.199: 4 Chirality restraints: 2797 Sorted by residual: chirality pdb=" CA ILE B 122 " pdb=" N ILE B 122 " pdb=" C ILE B 122 " pdb=" CB ILE B 122 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE A 831 " pdb=" N ILE A 831 " pdb=" C ILE A 831 " pdb=" CB ILE A 831 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA VAL B 117 " pdb=" N VAL B 117 " pdb=" C VAL B 117 " pdb=" CB VAL B 117 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2794 not shown) Planarity restraints: 5260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 684 " 0.697 9.50e-02 1.11e+02 2.33e-01 6.59e+01 pdb=" NE ARG A 684 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 684 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 684 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG A 684 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 684 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 684 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARG A 684 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 684 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 552 " -0.504 9.50e-02 1.11e+02 1.69e-01 3.67e+01 pdb=" NE ARG A 552 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 552 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 552 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 552 " 0.016 2.00e-02 2.50e+03 pdb="HH11 ARG A 552 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 552 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 552 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 552 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " 0.459 9.50e-02 1.11e+02 1.54e-01 2.86e+01 pdb=" NE ARG A 273 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG A 273 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 273 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 273 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 273 " 0.014 2.00e-02 2.50e+03 ... (remaining 5257 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 601 2.09 - 2.72: 61793 2.72 - 3.34: 100297 3.34 - 3.97: 129063 3.97 - 4.60: 203762 Nonbonded interactions: 495516 Sorted by model distance: nonbonded pdb="HD21 ASN A 430 " pdb=" OD1 ASN A 465 " model vdw 1.461 2.450 nonbonded pdb="HD22 ASN A 167 " pdb=" O THR A 506 " model vdw 1.497 2.450 nonbonded pdb=" HG SER E 147 " pdb=" O VAL E 187 " model vdw 1.536 2.450 nonbonded pdb=" H LEU A 44 " pdb=" O GLU A 55 " model vdw 1.544 2.450 nonbonded pdb=" HH TYR C 264 " pdb=" O ALA C 299 " model vdw 1.572 2.450 ... (remaining 495511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 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 : 0.003 0.049 18142 Z= 0.128 Angle : 0.626 6.688 24574 Z= 0.347 Chirality : 0.042 0.199 2797 Planarity : 0.010 0.299 3134 Dihedral : 13.507 123.604 6685 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.97 % Allowed : 6.51 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.58 (0.16), residues: 2186 helix: -1.76 (0.17), residues: 755 sheet: -1.34 (0.21), residues: 509 loop : -1.70 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG A 684 TYR 0.030 0.002 TYR A 935 PHE 0.026 0.002 PHE B 230 TRP 0.016 0.001 TRP A 413 HIS 0.008 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00264 (18142) covalent geometry : angle 0.62568 (24574) hydrogen bonds : bond 0.17860 ( 822) hydrogen bonds : angle 8.02846 ( 2421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8920 (mt) cc_final: 0.8702 (mp) REVERT: A 46 THR cc_start: 0.6167 (OUTLIER) cc_final: 0.5929 (p) REVERT: A 150 PHE cc_start: 0.8360 (t80) cc_final: 0.8107 (t80) REVERT: A 259 MET cc_start: 0.0667 (tpp) cc_final: 0.0465 (tpp) REVERT: A 369 ASP cc_start: 0.6920 (t0) cc_final: 0.6618 (t0) REVERT: A 435 CYS cc_start: 0.7082 (t) cc_final: 0.6599 (t) REVERT: A 521 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: A 657 LEU cc_start: 0.8374 (mt) cc_final: 0.7930 (tp) REVERT: A 728 MET cc_start: 0.7886 (mmm) cc_final: 0.7575 (mmm) REVERT: A 768 LYS cc_start: 0.8545 (mttt) cc_final: 0.8335 (mmtt) REVERT: A 860 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5763 (mp) REVERT: B 77 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 298 PHE cc_start: 0.8179 (m-80) cc_final: 0.7863 (m-10) REVERT: B 729 ILE cc_start: 0.8951 (mt) cc_final: 0.8460 (mp) REVERT: D 9 ILE cc_start: 0.5060 (mt) cc_final: 0.4652 (tt) REVERT: D 19 LEU cc_start: 0.7281 (mt) cc_final: 0.6966 (mt) outliers start: 58 outliers final: 22 residues processed: 392 average time/residue: 0.4032 time to fit residues: 221.7455 Evaluate side-chains 236 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 798 LYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 220 GLN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN A1007 GLN B 190 HIS B 309 GLN D 4 ASN D 18 GLN F 4 ASN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.137683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.100096 restraints weight = 159704.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.103748 restraints weight = 62048.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.105991 restraints weight = 35618.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.107273 restraints weight = 25711.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.108049 restraints weight = 21367.276| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18142 Z= 0.224 Angle : 0.661 6.990 24574 Z= 0.353 Chirality : 0.043 0.175 2797 Planarity : 0.005 0.066 3134 Dihedral : 6.803 72.930 2470 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 2.92 % Allowed : 11.48 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.86 (0.17), residues: 2186 helix: -0.57 (0.18), residues: 782 sheet: -1.19 (0.22), residues: 516 loop : -1.73 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 146 TYR 0.020 0.002 TYR A 720 PHE 0.030 0.002 PHE B 688 TRP 0.014 0.002 TRP A 576 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00496 (18142) covalent geometry : angle 0.66145 (24574) hydrogen bonds : bond 0.05238 ( 822) hydrogen bonds : angle 6.10247 ( 2421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4734 (t80) REVERT: C 188 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.6158 (mmm) REVERT: A 384 GLU cc_start: 0.7038 (tt0) cc_final: 0.6711 (tm-30) REVERT: A 657 LEU cc_start: 0.8402 (mt) cc_final: 0.7974 (tp) REVERT: B 125 GLU cc_start: 0.8138 (tp30) cc_final: 0.7869 (tp30) REVERT: B 165 LEU cc_start: 0.8292 (mp) cc_final: 0.7805 (tp) REVERT: B 298 PHE cc_start: 0.8150 (m-80) cc_final: 0.7851 (m-10) outliers start: 57 outliers final: 44 residues processed: 258 average time/residue: 0.3655 time to fit residues: 136.1591 Evaluate side-chains 229 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 985 PHE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 59 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 69 GLN A 231 GLN A 646 GLN A 705 GLN A 735 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.144439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.105063 restraints weight = 172266.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.108614 restraints weight = 72371.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.110458 restraints weight = 42855.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.111484 restraints weight = 31939.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.111958 restraints weight = 27451.536| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18142 Z= 0.183 Angle : 0.603 6.183 24574 Z= 0.319 Chirality : 0.042 0.164 2797 Planarity : 0.005 0.058 3134 Dihedral : 5.820 57.163 2442 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.33 % Allowed : 12.45 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.39 (0.17), residues: 2186 helix: 0.11 (0.18), residues: 781 sheet: -1.05 (0.22), residues: 511 loop : -1.70 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 251 TYR 0.015 0.002 TYR A 100 PHE 0.023 0.002 PHE B 129 TRP 0.011 0.001 TRP E 297 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00406 (18142) covalent geometry : angle 0.60347 (24574) hydrogen bonds : bond 0.04554 ( 822) hydrogen bonds : angle 5.57948 ( 2421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.4720 (t80) REVERT: A 70 MET cc_start: 0.8190 (ttp) cc_final: 0.7908 (tmm) REVERT: A 384 GLU cc_start: 0.6890 (tt0) cc_final: 0.6666 (tm-30) REVERT: A 546 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8630 (mm-30) REVERT: A 547 MET cc_start: 0.7704 (ptp) cc_final: 0.7335 (ptm) REVERT: A 657 LEU cc_start: 0.8384 (mt) cc_final: 0.7970 (tp) REVERT: B 165 LEU cc_start: 0.8345 (mp) cc_final: 0.7819 (tp) REVERT: B 298 PHE cc_start: 0.8651 (m-80) cc_final: 0.8441 (m-80) outliers start: 65 outliers final: 41 residues processed: 234 average time/residue: 0.3422 time to fit residues: 117.8959 Evaluate side-chains 217 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain D residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 56 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 39 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** F 59 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 = 0.4850 r_free = 0.4850 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.107822 restraints weight = 169585.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.111358 restraints weight = 68097.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.113469 restraints weight = 39537.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 82)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.114570 restraints weight = 28943.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.115105 restraints weight = 24910.973| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18142 Z= 0.101 Angle : 0.519 5.872 24574 Z= 0.268 Chirality : 0.040 0.160 2797 Planarity : 0.004 0.092 3134 Dihedral : 5.146 50.953 2436 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.10 % Allowed : 13.27 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.18), residues: 2186 helix: 0.92 (0.18), residues: 785 sheet: -0.93 (0.22), residues: 503 loop : -1.34 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.013 0.001 TYR C 124 PHE 0.018 0.001 PHE B 688 TRP 0.012 0.001 TRP E 297 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00221 (18142) covalent geometry : angle 0.51947 (24574) hydrogen bonds : bond 0.03647 ( 822) hydrogen bonds : angle 5.04662 ( 2421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.4796 (t80) REVERT: A 70 MET cc_start: 0.8040 (ttp) cc_final: 0.7806 (tmm) REVERT: A 150 PHE cc_start: 0.7968 (t80) cc_final: 0.7738 (t80) REVERT: A 384 GLU cc_start: 0.6729 (tt0) cc_final: 0.6475 (tm-30) REVERT: A 521 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6332 (m-30) REVERT: A 657 LEU cc_start: 0.8185 (mt) cc_final: 0.7780 (tp) REVERT: B 165 LEU cc_start: 0.8281 (mp) cc_final: 0.7743 (tp) REVERT: F 38 MET cc_start: 0.5930 (ttp) cc_final: 0.5684 (mtp) outliers start: 41 outliers final: 28 residues processed: 207 average time/residue: 0.3452 time to fit residues: 105.6088 Evaluate side-chains 197 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 4 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 166 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.144026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.109538 restraints weight = 171627.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.112601 restraints weight = 81111.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.113792 restraints weight = 48405.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.114315 restraints weight = 37257.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.114395 restraints weight = 31705.982| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18142 Z= 0.166 Angle : 0.561 7.013 24574 Z= 0.293 Chirality : 0.041 0.152 2797 Planarity : 0.004 0.048 3134 Dihedral : 5.156 53.647 2432 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.61 % Allowed : 13.42 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.82 (0.18), residues: 2186 helix: 0.87 (0.18), residues: 784 sheet: -0.94 (0.22), residues: 501 loop : -1.52 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.016 0.002 TYR B 730 PHE 0.023 0.002 PHE A 985 TRP 0.012 0.001 TRP E 297 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00368 (18142) covalent geometry : angle 0.56073 (24574) hydrogen bonds : bond 0.04016 ( 822) hydrogen bonds : angle 5.07744 ( 2421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5171 (t80) REVERT: A 70 MET cc_start: 0.8506 (ttp) cc_final: 0.7989 (tmm) REVERT: A 546 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8710 (mm-30) REVERT: A 657 LEU cc_start: 0.8359 (mt) cc_final: 0.7922 (tp) REVERT: A 812 TRP cc_start: 0.7117 (t-100) cc_final: 0.6877 (t-100) REVERT: A 842 MET cc_start: 0.6128 (ttm) cc_final: 0.5914 (ttm) REVERT: B 165 LEU cc_start: 0.8208 (mp) cc_final: 0.7659 (tp) outliers start: 51 outliers final: 42 residues processed: 199 average time/residue: 0.3420 time to fit residues: 100.8557 Evaluate side-chains 206 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 48 optimal weight: 7.9990 chunk 214 optimal weight: 40.0000 chunk 174 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 340 ASN E 230 ASN E 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.107647 restraints weight = 171763.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.110546 restraints weight = 86561.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.110457 restraints weight = 50157.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.111257 restraints weight = 47120.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.111325 restraints weight = 39752.927| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18142 Z= 0.235 Angle : 0.635 7.963 24574 Z= 0.338 Chirality : 0.043 0.169 2797 Planarity : 0.005 0.052 3134 Dihedral : 5.558 62.087 2432 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.12 % Allowed : 13.83 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.18 (0.17), residues: 2186 helix: 0.51 (0.18), residues: 778 sheet: -1.13 (0.22), residues: 515 loop : -1.67 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 154 TYR 0.017 0.002 TYR A 100 PHE 0.029 0.002 PHE B 129 TRP 0.015 0.002 TRP A 697 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00521 (18142) covalent geometry : angle 0.63529 (24574) hydrogen bonds : bond 0.04568 ( 822) hydrogen bonds : angle 5.32024 ( 2421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5533 (t80) REVERT: A 70 MET cc_start: 0.8469 (ttp) cc_final: 0.7935 (tmm) REVERT: A 546 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: A 657 LEU cc_start: 0.8498 (mt) cc_final: 0.8033 (tp) REVERT: A 842 MET cc_start: 0.6546 (ttm) cc_final: 0.6337 (ttm) REVERT: B 10 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.4203 (mm-30) REVERT: B 165 LEU cc_start: 0.8237 (mp) cc_final: 0.7692 (tp) REVERT: D 9 ILE cc_start: 0.4554 (tt) cc_final: 0.4284 (pt) outliers start: 61 outliers final: 50 residues processed: 207 average time/residue: 0.3171 time to fit residues: 98.3553 Evaluate side-chains 208 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain D residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN E 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.143319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.109255 restraints weight = 170863.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.111945 restraints weight = 80514.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.113526 restraints weight = 47923.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.113800 restraints weight = 37756.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.114151 restraints weight = 32271.628| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18142 Z= 0.120 Angle : 0.532 6.524 24574 Z= 0.276 Chirality : 0.040 0.169 2797 Planarity : 0.004 0.046 3134 Dihedral : 5.203 57.838 2432 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.25 % Allowed : 14.86 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.80 (0.18), residues: 2186 helix: 1.01 (0.18), residues: 792 sheet: -1.00 (0.22), residues: 505 loop : -1.62 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 738 TYR 0.014 0.001 TYR B 730 PHE 0.023 0.001 PHE B 175 TRP 0.009 0.001 TRP A 812 HIS 0.004 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00268 (18142) covalent geometry : angle 0.53241 (24574) hydrogen bonds : bond 0.03699 ( 822) hydrogen bonds : angle 4.93158 ( 2421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 GLU cc_start: 0.7892 (tp30) cc_final: 0.7545 (tp30) REVERT: C 105 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.5533 (t80) REVERT: E 325 MET cc_start: 0.4085 (mmm) cc_final: 0.3739 (mmm) REVERT: A 70 MET cc_start: 0.8461 (ttp) cc_final: 0.7917 (tmm) REVERT: A 546 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8771 (mm-30) REVERT: A 657 LEU cc_start: 0.8269 (mt) cc_final: 0.7841 (tp) REVERT: A 842 MET cc_start: 0.6146 (ttm) cc_final: 0.5926 (ttm) REVERT: B 165 LEU cc_start: 0.8162 (mp) cc_final: 0.7626 (tp) REVERT: D 9 ILE cc_start: 0.4291 (tt) cc_final: 0.4033 (pt) outliers start: 44 outliers final: 37 residues processed: 194 average time/residue: 0.3181 time to fit residues: 93.0614 Evaluate side-chains 196 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 21 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 22 optimal weight: 0.0270 chunk 132 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 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 = 0.4833 r_free = 0.4833 target = 0.144549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.111039 restraints weight = 169792.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.114637 restraints weight = 78903.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.114666 restraints weight = 46223.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.115246 restraints weight = 45025.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.115334 restraints weight = 37083.272| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18142 Z= 0.102 Angle : 0.514 5.812 24574 Z= 0.263 Chirality : 0.040 0.156 2797 Planarity : 0.004 0.043 3134 Dihedral : 4.941 55.585 2430 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.95 % Allowed : 15.78 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.44 (0.18), residues: 2186 helix: 1.40 (0.19), residues: 794 sheet: -0.91 (0.22), residues: 506 loop : -1.44 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.013 0.001 TYR B 730 PHE 0.019 0.001 PHE B 175 TRP 0.032 0.001 TRP A 812 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00233 (18142) covalent geometry : angle 0.51354 (24574) hydrogen bonds : bond 0.03377 ( 822) hydrogen bonds : angle 4.71856 ( 2421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 GLU cc_start: 0.8019 (tp30) cc_final: 0.7615 (tp30) REVERT: C 68 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8912 (mtm110) REVERT: C 105 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5620 (t80) REVERT: E 325 MET cc_start: 0.4488 (mmm) cc_final: 0.4244 (mmm) REVERT: A 70 MET cc_start: 0.8439 (ttp) cc_final: 0.7900 (tmm) REVERT: A 150 PHE cc_start: 0.8051 (t80) cc_final: 0.7788 (t80) REVERT: A 546 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8714 (mm-30) REVERT: A 657 LEU cc_start: 0.8201 (mt) cc_final: 0.7808 (tp) REVERT: A 842 MET cc_start: 0.6014 (ttm) cc_final: 0.5788 (ttm) REVERT: B 165 LEU cc_start: 0.8127 (mp) cc_final: 0.7594 (tp) REVERT: D 9 ILE cc_start: 0.4304 (tt) cc_final: 0.4083 (pt) outliers start: 38 outliers final: 31 residues processed: 196 average time/residue: 0.3349 time to fit residues: 98.0095 Evaluate side-chains 197 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 26 optimal weight: 0.7980 chunk 213 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 62 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN F 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.144798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.111339 restraints weight = 169844.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.114942 restraints weight = 77668.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.114690 restraints weight = 46683.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.115369 restraints weight = 46065.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.115559 restraints weight = 37644.833| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18142 Z= 0.099 Angle : 0.504 6.514 24574 Z= 0.257 Chirality : 0.040 0.155 2797 Planarity : 0.003 0.043 3134 Dihedral : 4.800 54.189 2430 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.74 % Allowed : 15.83 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.18), residues: 2186 helix: 1.54 (0.19), residues: 798 sheet: -0.82 (0.22), residues: 515 loop : -1.35 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.013 0.001 TYR B 730 PHE 0.017 0.001 PHE B 175 TRP 0.021 0.001 TRP A 812 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00227 (18142) covalent geometry : angle 0.50368 (24574) hydrogen bonds : bond 0.03244 ( 822) hydrogen bonds : angle 4.60721 ( 2421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 GLU cc_start: 0.8050 (tp30) cc_final: 0.7650 (tp30) REVERT: C 68 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8961 (mtm110) REVERT: C 105 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5634 (t80) REVERT: C 325 MET cc_start: 0.7087 (tpp) cc_final: 0.6570 (tpp) REVERT: E 325 MET cc_start: 0.4467 (mmm) cc_final: 0.4259 (mmm) REVERT: A 70 MET cc_start: 0.8440 (ttp) cc_final: 0.7917 (tmm) REVERT: A 150 PHE cc_start: 0.8066 (t80) cc_final: 0.7825 (t80) REVERT: A 546 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: A 547 MET cc_start: 0.7797 (ptp) cc_final: 0.7528 (ptm) REVERT: A 657 LEU cc_start: 0.8195 (mt) cc_final: 0.7790 (tp) REVERT: A 842 MET cc_start: 0.5811 (ttm) cc_final: 0.5595 (ttm) REVERT: B 165 LEU cc_start: 0.8132 (mp) cc_final: 0.7598 (tp) REVERT: D 9 ILE cc_start: 0.4306 (tt) cc_final: 0.4090 (pt) outliers start: 34 outliers final: 29 residues processed: 189 average time/residue: 0.3221 time to fit residues: 91.8196 Evaluate side-chains 193 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 116 optimal weight: 0.3980 chunk 195 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.109819 restraints weight = 172227.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.112580 restraints weight = 85529.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.113250 restraints weight = 47191.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.113791 restraints weight = 44819.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.113868 restraints weight = 37987.718| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18142 Z= 0.149 Angle : 0.541 7.377 24574 Z= 0.280 Chirality : 0.041 0.146 2797 Planarity : 0.004 0.043 3134 Dihedral : 4.958 55.147 2430 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.90 % Allowed : 15.98 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.49 (0.18), residues: 2186 helix: 1.31 (0.19), residues: 795 sheet: -0.87 (0.22), residues: 505 loop : -1.48 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.014 0.001 TYR B 730 PHE 0.022 0.001 PHE B 175 TRP 0.020 0.001 TRP A 812 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00335 (18142) covalent geometry : angle 0.54056 (24574) hydrogen bonds : bond 0.03576 ( 822) hydrogen bonds : angle 4.75678 ( 2421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 GLU cc_start: 0.7987 (tp30) cc_final: 0.7600 (tp30) REVERT: C 68 ARG cc_start: 0.9219 (ttp80) cc_final: 0.8906 (mtm110) REVERT: C 105 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5604 (t80) REVERT: A 70 MET cc_start: 0.8394 (ttp) cc_final: 0.7869 (tmm) REVERT: A 150 PHE cc_start: 0.8067 (t80) cc_final: 0.7841 (t80) REVERT: A 546 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: A 657 LEU cc_start: 0.8317 (mt) cc_final: 0.7909 (tp) REVERT: B 165 LEU cc_start: 0.8227 (mp) cc_final: 0.7708 (tp) outliers start: 37 outliers final: 31 residues processed: 191 average time/residue: 0.3422 time to fit residues: 97.1298 Evaluate side-chains 197 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 202 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 259 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.137544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099589 restraints weight = 159451.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.103643 restraints weight = 57277.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.106086 restraints weight = 32163.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.107627 restraints weight = 23071.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.108530 restraints weight = 18920.669| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18142 Z= 0.140 Angle : 0.539 9.877 24574 Z= 0.278 Chirality : 0.041 0.148 2797 Planarity : 0.004 0.044 3134 Dihedral : 4.998 57.680 2430 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.90 % Allowed : 15.78 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.54 (0.18), residues: 2186 helix: 1.26 (0.19), residues: 789 sheet: -0.91 (0.22), residues: 506 loop : -1.47 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.014 0.001 TYR B 730 PHE 0.022 0.001 PHE B 175 TRP 0.018 0.001 TRP A 812 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00314 (18142) covalent geometry : angle 0.53886 (24574) hydrogen bonds : bond 0.03526 ( 822) hydrogen bonds : angle 4.75429 ( 2421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7607.48 seconds wall clock time: 130 minutes 25.77 seconds (7825.77 seconds total)