Starting phenix.real_space_refine on Sun Sep 13 14:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.map" model { file = "/net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s5t_54609/09_2026/9s5t_54609.cif" } resolution = 4.2 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= -0.053 sd= 1.207 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15126 2.51 5 N 3780 2.21 5 O 4387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23389 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5432 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 9, 'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 9, 'PHE:plan': 3, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2360 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 288} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1534 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1184 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1007 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 813 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1329 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 158} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1052 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8484 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.20 Number of scatterers: 23389 At special positions: 0 Unit cell: (120.019, 177.901, 179.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4387 8.00 N 3780 7.00 C 15126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A 801 " - " ASN A 574 " " NAG A 802 " - " ASN A 202 " " NAG A 803 " - " ASN A 192 " " NAG G 301 " - " ASN G 67 " " NAG G 302 " - " ASN G 97 " " NAG Z 1 " - " ASN A 73 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5642 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 30 sheets defined 44.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 247 through 269 Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.033A pdb=" N LYS A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 728 through 757 removed outlier: 3.961A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Proline residue: A 746 - end of helix Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.525A pdb=" N THR B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.661A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 64 removed outlier: 3.734A pdb=" N PHE B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.866A pdb=" N ALA B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.869A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 122 through 140 removed outlier: 3.913A pdb=" N TYR B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.745A pdb=" N ASP B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 removed outlier: 3.639A pdb=" N GLY B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 218 through 237 removed outlier: 3.553A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 256 removed outlier: 3.718A pdb=" N GLU B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 4.023A pdb=" N ALA B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.663A pdb=" N LYS B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.913A pdb=" N LYS C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 33 Processing helix chain 'C' and resid 43 through 62 Processing helix chain 'C' and resid 63 through 66 removed outlier: 3.724A pdb=" N LEU C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 66' Processing helix chain 'C' and resid 67 through 85 Processing helix chain 'C' and resid 112 through 140 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.002A pdb=" N TRP C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 18 through 22 removed outlier: 3.637A pdb=" N TYR D 22 " --> pdb=" O ILE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 78 through 94 Proline residue: D 85 - end of helix removed outlier: 3.799A pdb=" N MET D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 120 Proline residue: D 113 - end of helix Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 133 through 162 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'E' and resid 2 through 33 removed outlier: 3.614A pdb=" N LYS E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 removed outlier: 3.660A pdb=" N MET E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.562A pdb=" N ASN E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.942A pdb=" N ILE E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.687A pdb=" N PHE E 119 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 120 " --> pdb=" O PRO E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 116 through 120' Processing helix chain 'E' and resid 121 through 137 Processing helix chain 'F' and resid 13 through 42 removed outlier: 3.814A pdb=" N VAL F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 68 removed outlier: 3.957A pdb=" N PHE F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 76 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'F' and resid 88 through 108 Processing helix chain 'G' and resid 154 through 157 Processing helix chain 'G' and resid 158 through 167 Processing helix chain 'H' and resid 123 through 131 Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 46 through 51 Processing helix chain 'I' and resid 53 through 78 Proline residue: I 75 - end of helix removed outlier: 3.800A pdb=" N ASN I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 157 through 163 Processing helix chain 'I' and resid 170 through 178 Processing helix chain 'I' and resid 188 through 198 removed outlier: 3.655A pdb=" N LEU I 192 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 215 Processing helix chain 'I' and resid 217 through 247 removed outlier: 3.739A pdb=" N ARG I 247 " --> pdb=" O LEU I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 272 Processing helix chain 'I' and resid 332 through 336 removed outlier: 3.696A pdb=" N LYS I 335 " --> pdb=" O GLY I 332 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE I 336 " --> pdb=" O VAL I 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 332 through 336' Processing helix chain 'I' and resid 372 through 376 removed outlier: 3.515A pdb=" N GLU I 375 " --> pdb=" O THR I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 388 removed outlier: 3.954A pdb=" N TYR I 387 " --> pdb=" O ARG I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 424 removed outlier: 4.429A pdb=" N GLU I 398 " --> pdb=" O VAL I 394 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA I 399 " --> pdb=" O ASP I 395 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 408 " --> pdb=" O LEU I 404 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE I 409 " --> pdb=" O PHE I 405 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS I 423 " --> pdb=" O VAL I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 441 removed outlier: 3.651A pdb=" N ILE I 439 " --> pdb=" O CYS I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 448 No H-bonds generated for 'chain 'I' and resid 446 through 448' Processing helix chain 'I' and resid 449 through 466 removed outlier: 3.730A pdb=" N MET I 453 " --> pdb=" O MET I 449 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR I 466 " --> pdb=" O LEU I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 471 through 473 No H-bonds generated for 'chain 'I' and resid 471 through 473' Processing helix chain 'I' and resid 474 through 479 removed outlier: 3.573A pdb=" N GLY I 479 " --> pdb=" O ILE I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 532 removed outlier: 3.517A pdb=" N VAL I 528 " --> pdb=" O SER I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 557 Processing helix chain 'I' and resid 606 through 613 removed outlier: 3.884A pdb=" N GLU I 612 " --> pdb=" O GLU I 608 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG I 613 " --> pdb=" O THR I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 621 through 631 removed outlier: 3.559A pdb=" N LYS I 626 " --> pdb=" O ASP I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 647 through 653 removed outlier: 3.588A pdb=" N ASP I 653 " --> pdb=" O SER I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 655 through 660 Processing helix chain 'I' and resid 681 through 690 removed outlier: 3.858A pdb=" N SER I 690 " --> pdb=" O LEU I 686 " (cutoff:3.500A) Processing helix chain 'I' and resid 700 through 712 Processing helix chain 'I' and resid 753 through 758 Processing helix chain 'I' and resid 766 through 773 Processing helix chain 'I' and resid 778 through 785 removed outlier: 3.631A pdb=" N HIS I 785 " --> pdb=" O ASP I 781 " (cutoff:3.500A) Processing helix chain 'I' and resid 793 through 807 Processing helix chain 'I' and resid 820 through 827 removed outlier: 3.568A pdb=" N LYS I 825 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 972 through 1001 removed outlier: 3.545A pdb=" N ASN I 976 " --> pdb=" O SER I 972 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET I 991 " --> pdb=" O ASN I 987 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 993 " --> pdb=" O ILE I 989 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA I 996 " --> pdb=" O TYR I 992 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1012 removed outlier: 4.294A pdb=" N SER I1007 " --> pdb=" O ALA I1003 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I1009 " --> pdb=" O SER I1005 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA I1012 " --> pdb=" O ILE I1008 " (cutoff:3.500A) Processing helix chain 'I' and resid 1017 through 1036 Processing helix chain 'I' and resid 1055 through 1083 Processing helix chain 'I' and resid 1099 through 1120 removed outlier: 3.674A pdb=" N PHE I1117 " --> pdb=" O GLN I1113 " (cutoff:3.500A) Processing helix chain 'I' and resid 1133 through 1153 Processing helix chain 'I' and resid 1155 through 1162 removed outlier: 3.732A pdb=" N ASN I1159 " --> pdb=" O LEU I1155 " (cutoff:3.500A) Processing helix chain 'I' and resid 1168 through 1197 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.723A pdb=" N LYS A 45 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 81 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 73 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 79 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116 removed outlier: 7.379A pdb=" N ALA A 101 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 95 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.912A pdb=" N LYS A 175 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 188 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP A 210 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 226 removed outlier: 3.657A pdb=" N ASP A 221 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 324 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP A 315 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 322 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.923A pdb=" N TYR A 355 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 370 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 357 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 359 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 366 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 379 through 386 removed outlier: 6.701A pdb=" N LYS A 395 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 382 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 393 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 384 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLN A 391 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 445 through 453 removed outlier: 6.739A pdb=" N GLY A 438 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS A 451 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 436 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D 186 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 458 through 465 removed outlier: 3.657A pdb=" N VAL A 461 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 496 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR A 463 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA A 494 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 505 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU A 522 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 507 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 520 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 509 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU H 107 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 537 Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 609 removed outlier: 7.067A pdb=" N GLU A 624 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 607 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 622 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A 609 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A 620 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 667 through 668 removed outlier: 4.389A pdb=" N ILE A 667 " --> pdb=" O THR H 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.878A pdb=" N MET C 146 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 174 " --> pdb=" O MET C 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 54 through 60 removed outlier: 3.871A pdb=" N ASN G 59 " --> pdb=" O GLY G 5 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY G 5 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE G 134 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS G 8 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL G 136 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG G 10 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU G 138 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.937A pdb=" N TYR G 71 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 87 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA G 104 " --> pdb=" O MET G 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 31 through 38 removed outlier: 6.843A pdb=" N THR H 20 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE H 38 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU H 18 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 8 " --> pdb=" O PRO H 17 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 31 through 38 removed outlier: 6.843A pdb=" N THR H 20 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE H 38 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU H 18 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 8 " --> pdb=" O PRO H 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 85 through 92 removed outlier: 6.715A pdb=" N TYR H 73 " --> pdb=" O THR H 100 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR H 102 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU H 75 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG H 104 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL H 77 " --> pdb=" O ARG H 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AC4, first strand: chain 'I' and resid 12 through 18 removed outlier: 6.497A pdb=" N TYR I 102 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER I 15 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU I 100 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU I 17 " --> pdb=" O HIS I 98 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N HIS I 98 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'I' and resid 263 through 265 removed outlier: 4.677A pdb=" N LEU I 277 " --> pdb=" O PHE I 259 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP I 292 " --> pdb=" O THR I 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 314 through 316 removed outlier: 6.242A pdb=" N ASN I 303 " --> pdb=" O ALA I 345 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA I 345 " --> pdb=" O ASN I 303 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 692 through 695 removed outlier: 6.554A pdb=" N THR I 811 " --> pdb=" O VAL I 829 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE I 831 " --> pdb=" O THR I 811 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET I 813 " --> pdb=" O ILE I 831 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU I 833 " --> pdb=" O MET I 813 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY I 815 " --> pdb=" O LEU I 833 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 498 through 503 removed outlier: 6.740A pdb=" N ILE I 670 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU I 502 " --> pdb=" O PHE I 668 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE I 668 " --> pdb=" O LEU I 502 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N LEU I 663 " --> pdb=" O SER I 642 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N SER I 642 " --> pdb=" O LEU I 663 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE I 665 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER I 640 " --> pdb=" O PHE I 665 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY I 667 " --> pdb=" O LEU I 638 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU I 599 " --> pdb=" O LEU I 643 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG I 588 " --> pdb=" O PHE I 582 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE I 582 " --> pdb=" O ARG I 588 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA I 590 " --> pdb=" O PHE I 580 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER I 594 " --> pdb=" O ILE I 576 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE I 576 " --> pdb=" O SER I 594 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 498 through 503 removed outlier: 6.740A pdb=" N ILE I 670 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU I 502 " --> pdb=" O PHE I 668 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE I 668 " --> pdb=" O LEU I 502 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE I 665 " --> pdb=" O SER I 615 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 536 through 537 removed outlier: 3.797A pdb=" N VAL I 544 " --> pdb=" O VAL I 536 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 742 through 745 removed outlier: 4.512A pdb=" N VAL I 788 " --> pdb=" O ILE I 763 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3306 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: 4.29 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7360 1.34 - 1.46: 5484 1.46 - 1.58: 10897 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 23906 Sorted by residual: bond pdb=" CA ILE C 127 " pdb=" CB ILE C 127 " ideal model delta sigma weight residual 1.539 1.527 0.012 5.40e-03 3.43e+04 4.89e+00 bond pdb=" C65 AJP I1301 " pdb=" O64 AJP I1301 " ideal model delta sigma weight residual 1.373 1.414 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C26 AJP I1301 " pdb=" O25 AJP I1301 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C45 AJP I1301 " pdb=" O44 AJP I1301 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C35 AJP I1301 " pdb=" O34 AJP I1301 " ideal model delta sigma weight residual 1.380 1.408 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 23901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 31966 2.11 - 4.22: 471 4.22 - 6.33: 52 6.33 - 8.44: 21 8.44 - 10.55: 1 Bond angle restraints: 32511 Sorted by residual: angle pdb=" N ASN B 290 " pdb=" CA ASN B 290 " pdb=" C ASN B 290 " ideal model delta sigma weight residual 112.25 107.43 4.82 1.36e+00 5.41e-01 1.26e+01 angle pdb=" CB LYS A 751 " pdb=" CG LYS A 751 " pdb=" CD LYS A 751 " ideal model delta sigma weight residual 111.30 118.24 -6.94 2.30e+00 1.89e-01 9.11e+00 angle pdb=" CA LEU A 758 " pdb=" CB LEU A 758 " pdb=" CG LEU A 758 " ideal model delta sigma weight residual 116.30 126.85 -10.55 3.50e+00 8.16e-02 9.08e+00 angle pdb=" CA LYS A 751 " pdb=" CB LYS A 751 " pdb=" CG LYS A 751 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 109.34 115.38 -6.04 2.08e+00 2.31e-01 8.43e+00 ... (remaining 32506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 13260 17.39 - 34.78: 1042 34.78 - 52.17: 169 52.17 - 69.56: 30 69.56 - 86.95: 13 Dihedral angle restraints: 14514 sinusoidal: 5812 harmonic: 8702 Sorted by residual: dihedral pdb=" CA PHE I 465 " pdb=" C PHE I 465 " pdb=" N TYR I 466 " pdb=" CA TYR I 466 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TRP A 120 " pdb=" C TRP A 120 " pdb=" N PHE A 121 " pdb=" CA PHE A 121 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ALA I 478 " pdb=" C ALA I 478 " pdb=" N GLY I 479 " pdb=" CA GLY I 479 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3663 0.101 - 0.203: 147 0.203 - 0.304: 1 0.304 - 0.405: 1 0.405 - 0.506: 1 Chirality restraints: 3813 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 202 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.91e+00 chirality pdb=" C55 AJP I1301 " pdb=" C56 AJP I1301 " pdb=" O54 AJP I1301 " pdb=" O60 AJP I1301 " both_signs ideal model delta sigma weight residual False 2.13 2.45 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 3810 not shown) Planarity restraints: 4084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO D 80 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 290 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ASN B 290 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 290 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS B 291 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 159 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO B 160 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.030 5.00e-02 4.00e+02 ... (remaining 4081 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 771 2.72 - 3.27: 23291 3.27 - 3.81: 35311 3.81 - 4.36: 41555 4.36 - 4.90: 70838 Nonbonded interactions: 171766 Sorted by model distance: nonbonded pdb=" O63 AJP I1301 " pdb=" O75 AJP I1301 " model vdw 2.176 3.040 nonbonded pdb=" O LEU B 45 " pdb=" OG1 THR B 46 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU B 118 " pdb=" OH TYR B 126 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 82 " pdb=" OD2 ASP A 706 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP H 74 " pdb=" OG1 THR H 100 " model vdw 2.209 3.040 ... (remaining 171761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 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 0.042 23914 Z= 0.129 Angle : 0.635 13.077 32535 Z= 0.312 Chirality : 0.044 0.506 3813 Planarity : 0.004 0.082 4078 Dihedral : 12.722 86.954 8872 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.18 (0.15), residues: 2930 helix: 1.03 (0.15), residues: 1173 sheet: 0.88 (0.24), residues: 497 loop : -1.70 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 383 TYR 0.021 0.001 TYR I 254 PHE 0.021 0.001 PHE F 102 TRP 0.036 0.002 TRP A 112 HIS 0.009 0.001 HIS I 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (23906) covalent geometry : angle 0.61892 / 0.31 (32511) hydrogen bonds : bond 0.21849 / 14.56 ( 1126) hydrogen bonds : angle 6.83292 / 4.75 ( 3306) link_BETA1-4 : bond 0.00652 / 0.34 ( 2) link_BETA1-4 : angle 2.95927 / 1.55 ( 6) link_NAG-ASN : bond 0.00665 / 0.33 ( 6) link_NAG-ASN : angle 5.88942 / 3.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.8039 (p) cc_final: 0.7784 (t) REVERT: A 83 ASN cc_start: 0.8597 (m-40) cc_final: 0.8348 (m-40) REVERT: A 93 GLN cc_start: 0.8004 (pt0) cc_final: 0.7679 (pm20) REVERT: A 98 ASP cc_start: 0.7446 (t0) cc_final: 0.7245 (t0) REVERT: A 105 VAL cc_start: 0.7981 (p) cc_final: 0.7590 (m) REVERT: A 112 TRP cc_start: 0.6952 (p-90) cc_final: 0.6304 (p-90) REVERT: A 124 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6671 (tt0) REVERT: A 190 ASN cc_start: 0.7395 (t0) cc_final: 0.6939 (p0) REVERT: A 210 TRP cc_start: 0.8450 (p-90) cc_final: 0.8002 (p-90) REVERT: A 213 ASP cc_start: 0.7449 (t0) cc_final: 0.7136 (t0) REVERT: A 215 TRP cc_start: 0.8537 (p-90) cc_final: 0.8054 (p-90) REVERT: A 259 ASN cc_start: 0.8305 (m-40) cc_final: 0.7949 (m-40) REVERT: A 317 VAL cc_start: 0.8544 (t) cc_final: 0.8269 (p) REVERT: A 355 TYR cc_start: 0.7755 (p90) cc_final: 0.7496 (p90) REVERT: A 406 LEU cc_start: 0.7802 (tp) cc_final: 0.7219 (tt) REVERT: A 455 ASN cc_start: 0.8237 (t0) cc_final: 0.7095 (t0) REVERT: A 457 LYS cc_start: 0.7870 (pttm) cc_final: 0.7587 (ptpp) REVERT: A 458 GLU cc_start: 0.7364 (mp0) cc_final: 0.6701 (mp0) REVERT: A 569 ASP cc_start: 0.7926 (m-30) cc_final: 0.7638 (m-30) REVERT: A 578 ASN cc_start: 0.7610 (m-40) cc_final: 0.7096 (t0) REVERT: A 611 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8433 (mtmm) REVERT: A 625 LEU cc_start: 0.8403 (mt) cc_final: 0.8199 (mp) REVERT: A 684 ASP cc_start: 0.7069 (t0) cc_final: 0.6553 (p0) REVERT: A 701 CYS cc_start: 0.7848 (t) cc_final: 0.7423 (m) REVERT: B 43 SER cc_start: 0.8870 (m) cc_final: 0.8364 (p) REVERT: B 47 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6944 (mm-30) REVERT: B 110 GLU cc_start: 0.6497 (pp20) cc_final: 0.6289 (pp20) REVERT: B 175 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6076 (tp30) REVERT: B 176 MET cc_start: 0.5380 (mmm) cc_final: 0.4558 (mmm) REVERT: B 187 GLU cc_start: 0.7273 (pt0) cc_final: 0.7040 (pt0) REVERT: B 224 GLU cc_start: 0.6145 (tp30) cc_final: 0.5811 (tm-30) REVERT: B 264 LYS cc_start: 0.7598 (mmtp) cc_final: 0.7348 (mmtp) REVERT: B 272 GLU cc_start: 0.7553 (tt0) cc_final: 0.7011 (tm-30) REVERT: B 273 ILE cc_start: 0.8639 (tp) cc_final: 0.7969 (tp) REVERT: B 279 ASN cc_start: 0.7491 (t0) cc_final: 0.7233 (t0) REVERT: B 280 LYS cc_start: 0.7559 (tttm) cc_final: 0.7075 (ttmt) REVERT: C 13 LEU cc_start: 0.8302 (mp) cc_final: 0.8068 (mt) REVERT: C 31 THR cc_start: 0.8228 (m) cc_final: 0.7871 (m) REVERT: C 111 MET cc_start: -0.0868 (ttt) cc_final: -0.1304 (ttt) REVERT: C 116 MET cc_start: 0.7120 (ttm) cc_final: 0.6754 (ttm) REVERT: C 123 MET cc_start: 0.7031 (mtp) cc_final: 0.6411 (mtp) REVERT: C 171 VAL cc_start: 0.8375 (m) cc_final: 0.8154 (p) REVERT: D 103 ILE cc_start: 0.8404 (mt) cc_final: 0.8130 (mt) REVERT: D 104 MET cc_start: 0.7710 (mmp) cc_final: 0.7478 (mmp) REVERT: D 109 LEU cc_start: 0.8299 (mm) cc_final: 0.8066 (mm) REVERT: E 7 LEU cc_start: 0.7527 (tp) cc_final: 0.7202 (tt) REVERT: E 82 LYS cc_start: 0.7448 (mtmm) cc_final: 0.7163 (mtmm) REVERT: E 118 SER cc_start: 0.8466 (m) cc_final: 0.8234 (m) REVERT: H 83 ASN cc_start: 0.8439 (m110) cc_final: 0.8236 (m110) REVERT: H 127 LYS cc_start: 0.8541 (tttt) cc_final: 0.8209 (tttt) REVERT: I 74 MET cc_start: 0.5744 (tpp) cc_final: 0.5465 (tpp) REVERT: I 432 ILE cc_start: 0.7381 (tp) cc_final: 0.7170 (tp) REVERT: I 435 CYS cc_start: 0.8506 (m) cc_final: 0.8131 (m) REVERT: I 451 LEU cc_start: 0.8024 (pt) cc_final: 0.7746 (pp) REVERT: I 458 SER cc_start: 0.8186 (m) cc_final: 0.7632 (p) REVERT: I 643 LEU cc_start: 0.7152 (mp) cc_final: 0.6504 (tp) REVERT: I 690 SER cc_start: 0.7768 (m) cc_final: 0.7509 (p) REVERT: I 697 THR cc_start: 0.7948 (t) cc_final: 0.7696 (m) REVERT: I 803 THR cc_start: 0.6838 (m) cc_final: 0.5804 (p) REVERT: I 826 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7327 (tm-30) REVERT: I 976 ASN cc_start: 0.8335 (m-40) cc_final: 0.7931 (m-40) REVERT: I 999 CYS cc_start: 0.7437 (m) cc_final: 0.7225 (m) REVERT: I 1068 VAL cc_start: 0.7773 (p) cc_final: 0.7503 (t) REVERT: I 1119 VAL cc_start: 0.8187 (t) cc_final: 0.7961 (p) REVERT: I 1120 ASN cc_start: 0.7441 (t0) cc_final: 0.6860 (t0) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.1378 time to fit residues: 115.1635 Evaluate side-chains 464 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 491 ASN A 587 HIS A 670 ASN C 6 GLN C 161 GLN C 167 GLN D 69 GLN D 182 ASN E 79 ASN E 86 GLN H 83 ASN I 261 ASN I 428 GLN ** I 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113593 restraints weight = 44621.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115301 restraints weight = 28778.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116520 restraints weight = 20477.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116772 restraints weight = 17267.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117018 restraints weight = 15274.998| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23914 Z= 0.170 Angle : 0.625 10.753 32535 Z= 0.325 Chirality : 0.044 0.333 3813 Planarity : 0.004 0.071 4078 Dihedral : 5.810 49.094 3530 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 0.16 % Allowed : 2.16 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.08 (0.15), residues: 2930 helix: 1.47 (0.15), residues: 1203 sheet: 0.72 (0.24), residues: 507 loop : -1.76 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 723 TYR 0.020 0.002 TYR I1137 PHE 0.030 0.002 PHE I1032 TRP 0.019 0.001 TRP A 112 HIS 0.011 0.001 HIS I1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (23906) covalent geometry : angle 0.61642 / 0.32 (32511) hydrogen bonds : bond 0.06099 / 4.05 ( 1126) hydrogen bonds : angle 4.90535 / 3.40 ( 3306) link_BETA1-4 : bond 0.00348 / 0.17 ( 2) link_BETA1-4 : angle 2.64756 / 1.44 ( 6) link_NAG-ASN : bond 0.00577 / 0.27 ( 6) link_NAG-ASN : angle 4.06068 / 2.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 509 time to evaluate : 0.857 Fit side-chains REVERT: A 51 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7138 (ttm110) REVERT: A 65 THR cc_start: 0.8161 (p) cc_final: 0.7889 (t) REVERT: A 83 ASN cc_start: 0.8687 (m-40) cc_final: 0.8469 (m-40) REVERT: A 112 TRP cc_start: 0.7277 (p-90) cc_final: 0.7058 (p-90) REVERT: A 135 ILE cc_start: 0.8025 (mm) cc_final: 0.7694 (pt) REVERT: A 210 TRP cc_start: 0.8370 (p-90) cc_final: 0.7664 (p-90) REVERT: A 213 ASP cc_start: 0.7421 (t0) cc_final: 0.7109 (t0) REVERT: A 215 TRP cc_start: 0.8553 (p-90) cc_final: 0.8039 (p-90) REVERT: A 264 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 317 VAL cc_start: 0.8575 (t) cc_final: 0.8303 (p) REVERT: A 355 TYR cc_start: 0.7807 (p90) cc_final: 0.7551 (p90) REVERT: A 406 LEU cc_start: 0.7905 (tp) cc_final: 0.7397 (tt) REVERT: A 426 ILE cc_start: 0.8727 (mm) cc_final: 0.8506 (mm) REVERT: A 455 ASN cc_start: 0.7986 (t0) cc_final: 0.7570 (t0) REVERT: A 457 LYS cc_start: 0.7921 (pttm) cc_final: 0.7471 (pttm) REVERT: A 458 GLU cc_start: 0.7528 (mp0) cc_final: 0.6794 (mp0) REVERT: A 519 ILE cc_start: 0.8831 (mt) cc_final: 0.8619 (mm) REVERT: A 569 ASP cc_start: 0.7856 (m-30) cc_final: 0.7556 (m-30) REVERT: A 578 ASN cc_start: 0.7751 (m-40) cc_final: 0.7180 (t0) REVERT: A 611 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8393 (mtmm) REVERT: A 625 LEU cc_start: 0.8517 (mt) cc_final: 0.8312 (mp) REVERT: A 684 ASP cc_start: 0.7043 (t0) cc_final: 0.6443 (p0) REVERT: B 25 GLU cc_start: 0.7507 (mp0) cc_final: 0.7160 (mm-30) REVERT: B 34 MET cc_start: 0.7920 (mtp) cc_final: 0.7500 (ttm) REVERT: B 43 SER cc_start: 0.8642 (m) cc_final: 0.8140 (p) REVERT: B 109 LEU cc_start: 0.7297 (mm) cc_final: 0.7040 (mt) REVERT: B 110 GLU cc_start: 0.6815 (pp20) cc_final: 0.6269 (pp20) REVERT: B 133 LEU cc_start: 0.8054 (tp) cc_final: 0.7735 (tt) REVERT: B 142 ASN cc_start: 0.8117 (m-40) cc_final: 0.7908 (m-40) REVERT: B 175 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6365 (tp30) REVERT: B 176 MET cc_start: 0.5516 (mmm) cc_final: 0.5137 (mmm) REVERT: B 187 GLU cc_start: 0.7416 (pt0) cc_final: 0.7120 (pt0) REVERT: B 261 ASP cc_start: 0.7342 (m-30) cc_final: 0.6890 (m-30) REVERT: B 271 LYS cc_start: 0.8244 (mttp) cc_final: 0.7562 (mtmm) REVERT: B 272 GLU cc_start: 0.7764 (tt0) cc_final: 0.7146 (tm-30) REVERT: B 273 ILE cc_start: 0.8642 (tp) cc_final: 0.8027 (tp) REVERT: B 280 LYS cc_start: 0.7146 (tttm) cc_final: 0.6623 (ttpt) REVERT: C 13 LEU cc_start: 0.8190 (mp) cc_final: 0.7961 (mt) REVERT: C 54 GLN cc_start: 0.7432 (tt0) cc_final: 0.6787 (tt0) REVERT: C 111 MET cc_start: -0.0310 (ttt) cc_final: -0.1099 (ttt) REVERT: C 116 MET cc_start: 0.7091 (ttm) cc_final: 0.6744 (ttm) REVERT: C 123 MET cc_start: 0.6889 (mtp) cc_final: 0.6278 (mtp) REVERT: C 159 MET cc_start: 0.6969 (mpp) cc_final: 0.6709 (mpp) REVERT: C 171 VAL cc_start: 0.8427 (m) cc_final: 0.8170 (p) REVERT: D 103 ILE cc_start: 0.8293 (mt) cc_final: 0.7882 (tp) REVERT: D 104 MET cc_start: 0.7788 (mmp) cc_final: 0.7515 (mmp) REVERT: E 7 LEU cc_start: 0.7575 (tp) cc_final: 0.7360 (tt) REVERT: F 98 MET cc_start: 0.7852 (ttm) cc_final: 0.7608 (ttm) REVERT: G 12 ASP cc_start: 0.7277 (t0) cc_final: 0.7041 (t0) REVERT: H 83 ASN cc_start: 0.8437 (m-40) cc_final: 0.8206 (m110) REVERT: H 127 LYS cc_start: 0.8531 (tttt) cc_final: 0.8273 (tptt) REVERT: I 458 SER cc_start: 0.8324 (m) cc_final: 0.7908 (p) REVERT: I 477 PHE cc_start: 0.7954 (t80) cc_final: 0.7392 (t80) REVERT: I 547 PRO cc_start: 0.6314 (Cg_exo) cc_final: 0.6013 (Cg_endo) REVERT: I 608 GLU cc_start: 0.7533 (mp0) cc_final: 0.7193 (mm-30) REVERT: I 643 LEU cc_start: 0.7206 (mp) cc_final: 0.6568 (tp) REVERT: I 690 SER cc_start: 0.7885 (m) cc_final: 0.7555 (p) REVERT: I 797 LYS cc_start: 0.7542 (mttt) cc_final: 0.7320 (mttt) REVERT: I 826 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7113 (tm-30) REVERT: I 976 ASN cc_start: 0.8361 (m-40) cc_final: 0.7959 (m-40) REVERT: I 999 CYS cc_start: 0.7662 (m) cc_final: 0.7455 (m) REVERT: I 1015 LYS cc_start: 0.8257 (pttm) cc_final: 0.7941 (ptpp) REVERT: I 1068 VAL cc_start: 0.7726 (p) cc_final: 0.7453 (t) REVERT: I 1120 ASN cc_start: 0.7103 (t0) cc_final: 0.6778 (t0) REVERT: I 1155 LEU cc_start: 0.8247 (mp) cc_final: 0.7929 (mm) outliers start: 4 outliers final: 1 residues processed: 511 average time/residue: 0.1395 time to fit residues: 116.0001 Evaluate side-chains 468 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 131 optimal weight: 0.0050 chunk 239 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 220 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 261 ASN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 18 HIS ** I 514 HIS ** 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 = 0.3767 r_free = 0.3767 target = 0.136255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118538 restraints weight = 44258.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119850 restraints weight = 29421.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121100 restraints weight = 21899.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121355 restraints weight = 18503.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121519 restraints weight = 16026.866| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23914 Z= 0.120 Angle : 0.554 10.138 32535 Z= 0.285 Chirality : 0.042 0.309 3813 Planarity : 0.004 0.061 4078 Dihedral : 5.419 44.848 3530 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 0.08 % Allowed : 1.96 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.34 (0.16), residues: 2930 helix: 1.73 (0.15), residues: 1200 sheet: 0.87 (0.24), residues: 487 loop : -1.64 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 383 TYR 0.022 0.001 TYR I 466 PHE 0.015 0.001 PHE I 207 TRP 0.012 0.001 TRP A 338 HIS 0.009 0.001 HIS I1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (23906) covalent geometry : angle 0.54856 / 0.28 (32511) hydrogen bonds : bond 0.05095 / 3.39 ( 1126) hydrogen bonds : angle 4.52967 / 3.15 ( 3306) link_BETA1-4 : bond 0.00478 / 0.23 ( 2) link_BETA1-4 : angle 2.32003 / 1.25 ( 6) link_NAG-ASN : bond 0.00505 / 0.20 ( 6) link_NAG-ASN : angle 3.14728 / 1.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8133 (p) cc_final: 0.7752 (t) REVERT: A 210 TRP cc_start: 0.8412 (p-90) cc_final: 0.7608 (p-90) REVERT: A 213 ASP cc_start: 0.7409 (t0) cc_final: 0.7072 (t0) REVERT: A 215 TRP cc_start: 0.8567 (p-90) cc_final: 0.8067 (p-90) REVERT: A 264 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 355 TYR cc_start: 0.7756 (p90) cc_final: 0.7505 (p90) REVERT: A 406 LEU cc_start: 0.7885 (tp) cc_final: 0.7423 (tt) REVERT: A 426 ILE cc_start: 0.8730 (mm) cc_final: 0.8507 (mm) REVERT: A 455 ASN cc_start: 0.7939 (t0) cc_final: 0.7698 (t0) REVERT: A 458 GLU cc_start: 0.7489 (mp0) cc_final: 0.6948 (mp0) REVERT: A 512 THR cc_start: 0.8000 (p) cc_final: 0.7765 (p) REVERT: A 514 THR cc_start: 0.8445 (m) cc_final: 0.8000 (t) REVERT: A 519 ILE cc_start: 0.8827 (mt) cc_final: 0.8597 (mm) REVERT: A 569 ASP cc_start: 0.7856 (m-30) cc_final: 0.7594 (m-30) REVERT: A 578 ASN cc_start: 0.7731 (m-40) cc_final: 0.7184 (t0) REVERT: A 611 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8400 (mtmm) REVERT: A 625 LEU cc_start: 0.8534 (mt) cc_final: 0.8303 (mp) REVERT: A 684 ASP cc_start: 0.6943 (t0) cc_final: 0.6356 (p0) REVERT: B 25 GLU cc_start: 0.7470 (mp0) cc_final: 0.7119 (mp0) REVERT: B 43 SER cc_start: 0.8494 (m) cc_final: 0.8078 (p) REVERT: B 109 LEU cc_start: 0.7219 (mm) cc_final: 0.6900 (mt) REVERT: B 110 GLU cc_start: 0.6894 (pp20) cc_final: 0.6579 (pp20) REVERT: B 133 LEU cc_start: 0.7990 (tp) cc_final: 0.7671 (tt) REVERT: B 142 ASN cc_start: 0.8133 (m-40) cc_final: 0.7909 (m-40) REVERT: B 175 GLU cc_start: 0.6720 (tp30) cc_final: 0.6517 (tp30) REVERT: B 176 MET cc_start: 0.5424 (mmm) cc_final: 0.4914 (mmm) REVERT: B 187 GLU cc_start: 0.7474 (pt0) cc_final: 0.7224 (pt0) REVERT: B 269 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7949 (mmtm) REVERT: B 272 GLU cc_start: 0.7730 (tt0) cc_final: 0.7148 (tm-30) REVERT: B 273 ILE cc_start: 0.8568 (tp) cc_final: 0.7956 (tp) REVERT: B 280 LYS cc_start: 0.6902 (tttm) cc_final: 0.6697 (mtpt) REVERT: B 282 LYS cc_start: 0.8417 (mttt) cc_final: 0.8211 (ttmm) REVERT: C 7 LEU cc_start: 0.8314 (mm) cc_final: 0.8079 (mm) REVERT: C 13 LEU cc_start: 0.8103 (mp) cc_final: 0.7898 (mt) REVERT: C 29 ILE cc_start: 0.8294 (mt) cc_final: 0.8069 (mm) REVERT: C 54 GLN cc_start: 0.7349 (tt0) cc_final: 0.6686 (tt0) REVERT: C 111 MET cc_start: -0.0545 (ttt) cc_final: -0.1200 (ttt) REVERT: C 116 MET cc_start: 0.7163 (ttm) cc_final: 0.6825 (ttm) REVERT: C 123 MET cc_start: 0.6780 (mtp) cc_final: 0.6262 (mtp) REVERT: C 159 MET cc_start: 0.6868 (mpp) cc_final: 0.6448 (mpp) REVERT: C 171 VAL cc_start: 0.8407 (m) cc_final: 0.8156 (p) REVERT: D 86 MET cc_start: 0.6570 (tmm) cc_final: 0.5922 (tmm) REVERT: D 98 LEU cc_start: 0.8405 (tp) cc_final: 0.8201 (tt) REVERT: D 103 ILE cc_start: 0.8288 (mt) cc_final: 0.7885 (tp) REVERT: D 104 MET cc_start: 0.7847 (mmp) cc_final: 0.7546 (mmp) REVERT: D 164 LEU cc_start: 0.8850 (mm) cc_final: 0.8637 (mp) REVERT: F 98 MET cc_start: 0.7882 (ttm) cc_final: 0.7673 (ttt) REVERT: G 12 ASP cc_start: 0.7283 (t0) cc_final: 0.7057 (t0) REVERT: H 83 ASN cc_start: 0.8456 (m-40) cc_final: 0.8193 (m110) REVERT: H 127 LYS cc_start: 0.8490 (tttt) cc_final: 0.8219 (tptt) REVERT: I 435 CYS cc_start: 0.8347 (m) cc_final: 0.8050 (m) REVERT: I 458 SER cc_start: 0.8293 (m) cc_final: 0.7830 (p) REVERT: I 608 GLU cc_start: 0.7543 (mp0) cc_final: 0.7279 (mm-30) REVERT: I 643 LEU cc_start: 0.7219 (mp) cc_final: 0.6509 (tp) REVERT: I 690 SER cc_start: 0.7937 (m) cc_final: 0.7554 (p) REVERT: I 797 LYS cc_start: 0.7426 (mttt) cc_final: 0.7125 (mttt) REVERT: I 803 THR cc_start: 0.6005 (m) cc_final: 0.5514 (p) REVERT: I 826 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7230 (tm-30) REVERT: I 1015 LYS cc_start: 0.8235 (pttm) cc_final: 0.7888 (ptpp) REVERT: I 1068 VAL cc_start: 0.7490 (p) cc_final: 0.7193 (t) REVERT: I 1120 ASN cc_start: 0.7243 (t0) cc_final: 0.6835 (t0) REVERT: I 1127 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7913 (mtp180) REVERT: I 1155 LEU cc_start: 0.8387 (mp) cc_final: 0.8052 (mm) outliers start: 2 outliers final: 1 residues processed: 503 average time/residue: 0.1403 time to fit residues: 113.9099 Evaluate side-chains 454 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 452 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 280 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 675 HIS C 129 GLN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN H 50 ASN ** I 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1208 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112225 restraints weight = 44403.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113793 restraints weight = 29363.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115081 restraints weight = 21431.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115522 restraints weight = 18957.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115854 restraints weight = 14530.234| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23914 Z= 0.183 Angle : 0.608 10.728 32535 Z= 0.316 Chirality : 0.044 0.322 3813 Planarity : 0.004 0.055 4078 Dihedral : 5.494 45.097 3530 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.16), residues: 2930 helix: 1.65 (0.15), residues: 1206 sheet: 0.77 (0.24), residues: 478 loop : -1.73 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 383 TYR 0.018 0.002 TYR A 355 PHE 0.022 0.002 PHE I 499 TRP 0.039 0.002 TRP A 112 HIS 0.008 0.001 HIS I 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (23906) covalent geometry : angle 0.60305 / 0.31 (32511) hydrogen bonds : bond 0.05891 / 3.94 ( 1126) hydrogen bonds : angle 4.64434 / 3.22 ( 3306) link_BETA1-4 : bond 0.00431 / 0.23 ( 2) link_BETA1-4 : angle 2.03158 / 1.10 ( 6) link_NAG-ASN : bond 0.00505 / 0.24 ( 6) link_NAG-ASN : angle 3.01486 / 1.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 504 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8089 (p) cc_final: 0.7720 (t) REVERT: A 88 THR cc_start: 0.8315 (p) cc_final: 0.8009 (m) REVERT: A 98 ASP cc_start: 0.7281 (t0) cc_final: 0.7078 (t0) REVERT: A 169 LEU cc_start: 0.7108 (mt) cc_final: 0.6671 (mt) REVERT: A 210 TRP cc_start: 0.8431 (p-90) cc_final: 0.7672 (p-90) REVERT: A 213 ASP cc_start: 0.7442 (t0) cc_final: 0.7081 (t0) REVERT: A 215 TRP cc_start: 0.8631 (p-90) cc_final: 0.8121 (p-90) REVERT: A 264 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 289 THR cc_start: 0.7467 (p) cc_final: 0.7215 (t) REVERT: A 317 VAL cc_start: 0.8622 (t) cc_final: 0.8267 (p) REVERT: A 335 LYS cc_start: 0.8429 (mmmm) cc_final: 0.8102 (mmmm) REVERT: A 355 TYR cc_start: 0.7790 (p90) cc_final: 0.7533 (p90) REVERT: A 406 LEU cc_start: 0.7950 (tp) cc_final: 0.7564 (tt) REVERT: A 457 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7467 (mmpt) REVERT: A 458 GLU cc_start: 0.7215 (mp0) cc_final: 0.6987 (mp0) REVERT: A 514 THR cc_start: 0.8427 (m) cc_final: 0.8080 (t) REVERT: A 516 GLU cc_start: 0.7072 (tp30) cc_final: 0.6781 (tp30) REVERT: A 569 ASP cc_start: 0.7786 (m-30) cc_final: 0.7476 (m-30) REVERT: A 578 ASN cc_start: 0.7882 (m-40) cc_final: 0.7264 (t0) REVERT: A 611 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8415 (mtmm) REVERT: A 625 LEU cc_start: 0.8500 (mt) cc_final: 0.8263 (mp) REVERT: A 626 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6798 (tm-30) REVERT: A 648 MET cc_start: 0.6810 (mtm) cc_final: 0.6589 (mtm) REVERT: A 684 ASP cc_start: 0.6985 (t0) cc_final: 0.6434 (p0) REVERT: B 25 GLU cc_start: 0.7487 (mp0) cc_final: 0.7102 (mp0) REVERT: B 43 SER cc_start: 0.8605 (m) cc_final: 0.8100 (p) REVERT: B 54 MET cc_start: 0.7950 (ttm) cc_final: 0.7626 (ttm) REVERT: B 59 TYR cc_start: 0.8406 (m-80) cc_final: 0.8151 (m-80) REVERT: B 109 LEU cc_start: 0.7319 (mm) cc_final: 0.6894 (mt) REVERT: B 127 VAL cc_start: 0.8231 (m) cc_final: 0.7946 (p) REVERT: B 142 ASN cc_start: 0.8105 (m-40) cc_final: 0.7875 (m-40) REVERT: B 176 MET cc_start: 0.5593 (mmm) cc_final: 0.5153 (tmm) REVERT: B 269 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7978 (mmtm) REVERT: B 271 LYS cc_start: 0.8283 (mttp) cc_final: 0.7516 (mtmm) REVERT: B 272 GLU cc_start: 0.7746 (tt0) cc_final: 0.7288 (tm-30) REVERT: B 273 ILE cc_start: 0.8685 (tp) cc_final: 0.8217 (tp) REVERT: B 280 LYS cc_start: 0.7183 (tttm) cc_final: 0.6953 (mtpt) REVERT: C 29 ILE cc_start: 0.8331 (mt) cc_final: 0.8109 (mm) REVERT: C 54 GLN cc_start: 0.7349 (tt0) cc_final: 0.6695 (tt0) REVERT: C 111 MET cc_start: -0.0527 (ttt) cc_final: -0.1221 (ttt) REVERT: C 116 MET cc_start: 0.7092 (ttm) cc_final: 0.6776 (ttm) REVERT: C 123 MET cc_start: 0.6766 (mtp) cc_final: 0.6255 (mtp) REVERT: C 159 MET cc_start: 0.6862 (mpp) cc_final: 0.6348 (mpp) REVERT: C 171 VAL cc_start: 0.8442 (m) cc_final: 0.8192 (p) REVERT: C 182 ILE cc_start: 0.8210 (mm) cc_final: 0.7955 (mt) REVERT: D 86 MET cc_start: 0.6677 (tmm) cc_final: 0.5726 (tmm) REVERT: D 98 LEU cc_start: 0.8413 (tp) cc_final: 0.8207 (tt) REVERT: D 103 ILE cc_start: 0.8339 (mt) cc_final: 0.7938 (tp) REVERT: D 104 MET cc_start: 0.7818 (mmp) cc_final: 0.7444 (mmp) REVERT: D 109 LEU cc_start: 0.8105 (mm) cc_final: 0.7678 (mm) REVERT: F 98 MET cc_start: 0.7874 (ttm) cc_final: 0.7660 (ttt) REVERT: G 12 ASP cc_start: 0.7334 (t0) cc_final: 0.7041 (t0) REVERT: G 43 THR cc_start: 0.8680 (p) cc_final: 0.8430 (t) REVERT: G 132 PRO cc_start: 0.8219 (Cg_endo) cc_final: 0.7962 (Cg_exo) REVERT: H 120 LYS cc_start: 0.8128 (tttt) cc_final: 0.7837 (tttt) REVERT: H 127 LYS cc_start: 0.8446 (tttt) cc_final: 0.8174 (tptt) REVERT: I 435 CYS cc_start: 0.8287 (m) cc_final: 0.8055 (m) REVERT: I 458 SER cc_start: 0.8381 (m) cc_final: 0.7882 (p) REVERT: I 477 PHE cc_start: 0.7945 (t80) cc_final: 0.7569 (t80) REVERT: I 547 PRO cc_start: 0.6370 (Cg_exo) cc_final: 0.6064 (Cg_endo) REVERT: I 608 GLU cc_start: 0.7553 (mp0) cc_final: 0.7206 (mm-30) REVERT: I 643 LEU cc_start: 0.7276 (mp) cc_final: 0.6562 (tp) REVERT: I 690 SER cc_start: 0.7984 (m) cc_final: 0.7589 (p) REVERT: I 797 LYS cc_start: 0.7539 (mttt) cc_final: 0.7167 (mttt) REVERT: I 803 THR cc_start: 0.6427 (m) cc_final: 0.5579 (p) REVERT: I 826 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7296 (tm-30) REVERT: I 828 HIS cc_start: 0.7964 (m-70) cc_final: 0.7679 (m-70) REVERT: I 1015 LYS cc_start: 0.8233 (pttm) cc_final: 0.7813 (ptpp) REVERT: I 1068 VAL cc_start: 0.7792 (p) cc_final: 0.7476 (t) REVERT: I 1120 ASN cc_start: 0.7412 (t0) cc_final: 0.6914 (t0) outliers start: 2 outliers final: 1 residues processed: 506 average time/residue: 0.1565 time to fit residues: 127.7194 Evaluate side-chains 451 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 36 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 491 ASN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN H 83 ASN ** I 514 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.128610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111040 restraints weight = 44309.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112536 restraints weight = 28914.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113851 restraints weight = 20655.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114388 restraints weight = 16743.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114406 restraints weight = 14009.999| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23914 Z= 0.221 Angle : 0.657 13.781 32535 Z= 0.341 Chirality : 0.046 0.326 3813 Planarity : 0.004 0.053 4078 Dihedral : 5.653 45.920 3530 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 0.08 % Allowed : 1.36 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.07 (0.15), residues: 2930 helix: 1.53 (0.15), residues: 1195 sheet: 0.94 (0.25), residues: 458 loop : -1.84 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 82 TYR 0.019 0.002 TYR A 355 PHE 0.026 0.002 PHE I 499 TRP 0.028 0.002 TRP A 112 HIS 0.010 0.001 HIS I 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (23906) covalent geometry : angle 0.65357 / 0.34 (32511) hydrogen bonds : bond 0.06289 / 4.21 ( 1126) hydrogen bonds : angle 4.77921 / 3.32 ( 3306) link_BETA1-4 : bond 0.00487 / 0.24 ( 2) link_BETA1-4 : angle 2.01162 / 1.10 ( 6) link_NAG-ASN : bond 0.00459 / 0.23 ( 6) link_NAG-ASN : angle 2.90567 / 1.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 510 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7464 (mp0) cc_final: 0.7113 (mp0) REVERT: A 65 THR cc_start: 0.8096 (p) cc_final: 0.7778 (t) REVERT: A 100 ASN cc_start: 0.7845 (m110) cc_final: 0.7619 (m-40) REVERT: A 112 TRP cc_start: 0.7974 (p-90) cc_final: 0.7663 (p-90) REVERT: A 169 LEU cc_start: 0.6969 (mt) cc_final: 0.6434 (mt) REVERT: A 210 TRP cc_start: 0.8433 (p-90) cc_final: 0.7682 (p-90) REVERT: A 213 ASP cc_start: 0.7460 (t0) cc_final: 0.7065 (t0) REVERT: A 289 THR cc_start: 0.7484 (p) cc_final: 0.7281 (t) REVERT: A 316 MET cc_start: 0.7846 (mtp) cc_final: 0.7636 (mtp) REVERT: A 317 VAL cc_start: 0.8655 (t) cc_final: 0.8334 (p) REVERT: A 355 TYR cc_start: 0.7817 (p90) cc_final: 0.7617 (p90) REVERT: A 406 LEU cc_start: 0.7977 (tp) cc_final: 0.7634 (tt) REVERT: A 457 LYS cc_start: 0.7953 (mmpt) cc_final: 0.7449 (mmpt) REVERT: A 458 GLU cc_start: 0.7225 (mp0) cc_final: 0.6871 (mp0) REVERT: A 514 THR cc_start: 0.8472 (m) cc_final: 0.8052 (t) REVERT: A 569 ASP cc_start: 0.7731 (m-30) cc_final: 0.7398 (m-30) REVERT: A 578 ASN cc_start: 0.7938 (m-40) cc_final: 0.7270 (t0) REVERT: A 611 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8442 (mtmm) REVERT: A 684 ASP cc_start: 0.6976 (t0) cc_final: 0.6462 (p0) REVERT: B 25 GLU cc_start: 0.7502 (mp0) cc_final: 0.7087 (mp0) REVERT: B 36 ILE cc_start: 0.8489 (mm) cc_final: 0.8205 (mt) REVERT: B 45 LEU cc_start: 0.7870 (tp) cc_final: 0.7550 (tp) REVERT: B 54 MET cc_start: 0.7980 (ttm) cc_final: 0.7670 (ttm) REVERT: B 59 TYR cc_start: 0.8419 (m-80) cc_final: 0.8068 (m-80) REVERT: B 109 LEU cc_start: 0.7342 (mm) cc_final: 0.6969 (mt) REVERT: B 110 GLU cc_start: 0.6903 (pp20) cc_final: 0.6484 (pp20) REVERT: B 127 VAL cc_start: 0.8182 (m) cc_final: 0.7913 (p) REVERT: B 133 LEU cc_start: 0.7968 (tp) cc_final: 0.7595 (tt) REVERT: B 271 LYS cc_start: 0.8312 (mttp) cc_final: 0.7583 (mtmm) REVERT: B 272 GLU cc_start: 0.7750 (tt0) cc_final: 0.6892 (tp30) REVERT: B 280 LYS cc_start: 0.7276 (tttm) cc_final: 0.7028 (mtpt) REVERT: C 29 ILE cc_start: 0.8394 (mt) cc_final: 0.8147 (mm) REVERT: C 54 GLN cc_start: 0.7373 (tt0) cc_final: 0.6663 (tt0) REVERT: C 111 MET cc_start: -0.0603 (ttt) cc_final: -0.1223 (ttt) REVERT: C 116 MET cc_start: 0.7090 (ttm) cc_final: 0.6820 (ttm) REVERT: C 123 MET cc_start: 0.6819 (mtp) cc_final: 0.6299 (mtp) REVERT: C 159 MET cc_start: 0.6842 (mpp) cc_final: 0.6585 (mpp) REVERT: C 182 ILE cc_start: 0.8235 (mm) cc_final: 0.8031 (mt) REVERT: D 25 GLN cc_start: 0.6844 (mm110) cc_final: 0.6600 (mm110) REVERT: D 86 MET cc_start: 0.6549 (tmm) cc_final: 0.6033 (tmm) REVERT: D 103 ILE cc_start: 0.8308 (mt) cc_final: 0.8037 (tp) REVERT: D 104 MET cc_start: 0.7886 (mmp) cc_final: 0.7534 (mmp) REVERT: E 82 LYS cc_start: 0.7542 (mtmm) cc_final: 0.7296 (mtmm) REVERT: F 56 LEU cc_start: 0.8126 (mt) cc_final: 0.7908 (mm) REVERT: G 12 ASP cc_start: 0.7340 (t0) cc_final: 0.7021 (t0) REVERT: G 43 THR cc_start: 0.8655 (p) cc_final: 0.8390 (t) REVERT: G 132 PRO cc_start: 0.8228 (Cg_endo) cc_final: 0.7943 (Cg_exo) REVERT: H 120 LYS cc_start: 0.8301 (tttt) cc_final: 0.7995 (tttt) REVERT: H 127 LYS cc_start: 0.8406 (tttt) cc_final: 0.8174 (tptt) REVERT: I 435 CYS cc_start: 0.8259 (m) cc_final: 0.8013 (m) REVERT: I 458 SER cc_start: 0.8341 (m) cc_final: 0.7869 (p) REVERT: I 477 PHE cc_start: 0.7997 (t80) cc_final: 0.7473 (t80) REVERT: I 547 PRO cc_start: 0.6526 (Cg_exo) cc_final: 0.6285 (Cg_endo) REVERT: I 608 GLU cc_start: 0.7486 (mp0) cc_final: 0.7172 (mm-30) REVERT: I 690 SER cc_start: 0.8107 (m) cc_final: 0.7729 (p) REVERT: I 797 LYS cc_start: 0.7522 (mttt) cc_final: 0.7175 (mttp) REVERT: I 803 THR cc_start: 0.6079 (m) cc_final: 0.5592 (p) REVERT: I 826 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7337 (tm-30) REVERT: I 828 HIS cc_start: 0.8028 (m-70) cc_final: 0.7583 (m-70) REVERT: I 1008 ILE cc_start: 0.8879 (tp) cc_final: 0.8607 (tp) REVERT: I 1015 LYS cc_start: 0.8276 (pttm) cc_final: 0.8026 (ptpp) REVERT: I 1068 VAL cc_start: 0.7855 (p) cc_final: 0.7497 (t) REVERT: I 1120 ASN cc_start: 0.7332 (t0) cc_final: 0.6858 (t0) REVERT: I 1127 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7929 (mtp180) REVERT: I 1155 LEU cc_start: 0.8480 (mt) cc_final: 0.8232 (mm) outliers start: 2 outliers final: 1 residues processed: 512 average time/residue: 0.1455 time to fit residues: 119.7307 Evaluate side-chains 463 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 196 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 118 HIS C 147 GLN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS D 69 GLN G 103 ASN H 83 ASN ** I 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115256 restraints weight = 44412.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116665 restraints weight = 28957.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118468 restraints weight = 21133.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118702 restraints weight = 16541.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118832 restraints weight = 14274.181| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23914 Z= 0.144 Angle : 0.590 11.396 32535 Z= 0.303 Chirality : 0.043 0.314 3813 Planarity : 0.004 0.051 4078 Dihedral : 5.417 43.385 3530 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 1.12 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.16), residues: 2930 helix: 1.71 (0.15), residues: 1204 sheet: 0.91 (0.24), residues: 469 loop : -1.82 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 383 TYR 0.021 0.001 TYR I 621 PHE 0.025 0.001 PHE I 144 TRP 0.024 0.001 TRP I 137 HIS 0.005 0.001 HIS I 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23906) covalent geometry : angle 0.58604 / 0.30 (32511) hydrogen bonds : bond 0.05372 / 3.58 ( 1126) hydrogen bonds : angle 4.53899 / 3.16 ( 3306) link_BETA1-4 : bond 0.00301 / 0.15 ( 2) link_BETA1-4 : angle 1.78776 / 0.97 ( 6) link_NAG-ASN : bond 0.00412 / 0.16 ( 6) link_NAG-ASN : angle 2.60756 / 1.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8007 (p) cc_final: 0.7627 (t) REVERT: A 97 ASN cc_start: 0.8244 (m-40) cc_final: 0.8043 (m-40) REVERT: A 112 TRP cc_start: 0.7970 (p-90) cc_final: 0.7636 (p-90) REVERT: A 169 LEU cc_start: 0.6941 (mt) cc_final: 0.6401 (mt) REVERT: A 210 TRP cc_start: 0.8369 (p-90) cc_final: 0.7595 (p-90) REVERT: A 213 ASP cc_start: 0.7464 (t0) cc_final: 0.7035 (t0) REVERT: A 316 MET cc_start: 0.7785 (mtp) cc_final: 0.7584 (mtp) REVERT: A 317 VAL cc_start: 0.8648 (t) cc_final: 0.8316 (p) REVERT: A 335 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8099 (mmmm) REVERT: A 355 TYR cc_start: 0.7809 (p90) cc_final: 0.7600 (p90) REVERT: A 406 LEU cc_start: 0.7927 (tp) cc_final: 0.7596 (tt) REVERT: A 455 ASN cc_start: 0.7989 (t0) cc_final: 0.7706 (t0) REVERT: A 457 LYS cc_start: 0.7953 (mmpt) cc_final: 0.7438 (mmpt) REVERT: A 458 GLU cc_start: 0.7202 (mp0) cc_final: 0.6518 (mp0) REVERT: A 514 THR cc_start: 0.8516 (m) cc_final: 0.7969 (t) REVERT: A 516 GLU cc_start: 0.7174 (tp30) cc_final: 0.6899 (tp30) REVERT: A 569 ASP cc_start: 0.7734 (m-30) cc_final: 0.7420 (m-30) REVERT: A 578 ASN cc_start: 0.7896 (m-40) cc_final: 0.7249 (t0) REVERT: A 611 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8479 (mtmm) REVERT: A 684 ASP cc_start: 0.6980 (t0) cc_final: 0.6430 (p0) REVERT: A 745 ARG cc_start: 0.7402 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: B 25 GLU cc_start: 0.7461 (mp0) cc_final: 0.7144 (mp0) REVERT: B 36 ILE cc_start: 0.8486 (mm) cc_final: 0.8168 (mt) REVERT: B 54 MET cc_start: 0.7978 (ttm) cc_final: 0.7663 (ttm) REVERT: B 109 LEU cc_start: 0.7289 (mm) cc_final: 0.6890 (mt) REVERT: B 127 VAL cc_start: 0.8111 (m) cc_final: 0.7824 (p) REVERT: B 133 LEU cc_start: 0.7948 (tp) cc_final: 0.7594 (tt) REVERT: B 271 LYS cc_start: 0.8310 (mttp) cc_final: 0.7524 (mtmm) REVERT: B 272 GLU cc_start: 0.7642 (tt0) cc_final: 0.7145 (tm-30) REVERT: B 273 ILE cc_start: 0.8711 (tp) cc_final: 0.8121 (tp) REVERT: B 280 LYS cc_start: 0.7155 (tttm) cc_final: 0.6858 (mtmt) REVERT: C 29 ILE cc_start: 0.8361 (mt) cc_final: 0.8122 (mm) REVERT: C 111 MET cc_start: -0.0422 (ttt) cc_final: -0.1110 (ttt) REVERT: C 116 MET cc_start: 0.7112 (ttm) cc_final: 0.6816 (ttm) REVERT: C 123 MET cc_start: 0.6744 (mtp) cc_final: 0.6221 (mtp) REVERT: C 182 ILE cc_start: 0.8161 (mm) cc_final: 0.7934 (mt) REVERT: D 86 MET cc_start: 0.6674 (tmm) cc_final: 0.5906 (tmm) REVERT: D 103 ILE cc_start: 0.8326 (mt) cc_final: 0.8000 (tp) REVERT: D 104 MET cc_start: 0.7775 (mmp) cc_final: 0.7460 (mmp) REVERT: D 109 LEU cc_start: 0.8049 (mm) cc_final: 0.7640 (mm) REVERT: F 56 LEU cc_start: 0.8086 (mt) cc_final: 0.7877 (mm) REVERT: G 12 ASP cc_start: 0.7365 (t0) cc_final: 0.7003 (t0) REVERT: G 43 THR cc_start: 0.8610 (p) cc_final: 0.8376 (t) REVERT: H 120 LYS cc_start: 0.8397 (tttt) cc_final: 0.7993 (tttt) REVERT: H 127 LYS cc_start: 0.8420 (tttt) cc_final: 0.8206 (tptt) REVERT: I 458 SER cc_start: 0.8250 (m) cc_final: 0.7905 (p) REVERT: I 477 PHE cc_start: 0.7939 (t80) cc_final: 0.7406 (t80) REVERT: I 547 PRO cc_start: 0.6505 (Cg_exo) cc_final: 0.6213 (Cg_endo) REVERT: I 643 LEU cc_start: 0.7288 (mt) cc_final: 0.6871 (tp) REVERT: I 690 SER cc_start: 0.8049 (m) cc_final: 0.7742 (p) REVERT: I 797 LYS cc_start: 0.7457 (mttt) cc_final: 0.7171 (mttp) REVERT: I 803 THR cc_start: 0.5986 (m) cc_final: 0.5601 (p) REVERT: I 828 HIS cc_start: 0.8041 (m-70) cc_final: 0.7592 (m-70) REVERT: I 1015 LYS cc_start: 0.8255 (pttm) cc_final: 0.7821 (ptpp) REVERT: I 1068 VAL cc_start: 0.7777 (p) cc_final: 0.7412 (t) REVERT: I 1120 ASN cc_start: 0.7420 (t0) cc_final: 0.6899 (t0) REVERT: I 1127 ARG cc_start: 0.8316 (mtm180) cc_final: 0.8038 (mtp180) REVERT: I 1155 LEU cc_start: 0.8448 (mt) cc_final: 0.8228 (mm) outliers start: 1 outliers final: 1 residues processed: 515 average time/residue: 0.1346 time to fit residues: 111.9654 Evaluate side-chains 454 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 93 GLN A 154 HIS A 675 HIS C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 86 GLN H 83 ASN ** I 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 595 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110930 restraints weight = 44239.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112306 restraints weight = 29446.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113488 restraints weight = 21498.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113925 restraints weight = 18369.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113983 restraints weight = 15324.808| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23914 Z= 0.273 Angle : 0.727 12.803 32535 Z= 0.380 Chirality : 0.048 0.331 3813 Planarity : 0.005 0.052 4078 Dihedral : 5.895 47.208 3530 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.20 (0.15), residues: 2930 helix: 1.33 (0.15), residues: 1198 sheet: 0.78 (0.25), residues: 459 loop : -2.02 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 383 TYR 0.023 0.002 TYR A 355 PHE 0.032 0.002 PHE I 499 TRP 0.041 0.002 TRP I 137 HIS 0.012 0.002 HIS I 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.27 (23906) covalent geometry : angle 0.72390 / 0.38 (32511) hydrogen bonds : bond 0.07265 / 4.86 ( 1126) hydrogen bonds : angle 5.00945 / 3.47 ( 3306) link_BETA1-4 : bond 0.00222 / 0.12 ( 2) link_BETA1-4 : angle 1.80170 / 0.98 ( 6) link_NAG-ASN : bond 0.00546 / 0.30 ( 6) link_NAG-ASN : angle 2.84317 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8156 (p) cc_final: 0.7795 (t) REVERT: A 97 ASN cc_start: 0.8275 (m-40) cc_final: 0.8017 (m-40) REVERT: A 169 LEU cc_start: 0.6948 (mt) cc_final: 0.6349 (mt) REVERT: A 210 TRP cc_start: 0.8425 (p-90) cc_final: 0.7738 (p-90) REVERT: A 213 ASP cc_start: 0.7477 (t0) cc_final: 0.7022 (t0) REVERT: A 316 MET cc_start: 0.7916 (mtp) cc_final: 0.7627 (mtp) REVERT: A 317 VAL cc_start: 0.8664 (t) cc_final: 0.8345 (p) REVERT: A 355 TYR cc_start: 0.7905 (p90) cc_final: 0.7703 (p90) REVERT: A 406 LEU cc_start: 0.7985 (tp) cc_final: 0.7667 (tt) REVERT: A 455 ASN cc_start: 0.7997 (t0) cc_final: 0.7703 (t0) REVERT: A 457 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7527 (mmpt) REVERT: A 514 THR cc_start: 0.8537 (m) cc_final: 0.8165 (t) REVERT: A 516 GLU cc_start: 0.7076 (tp30) cc_final: 0.6740 (tp30) REVERT: A 569 ASP cc_start: 0.7625 (m-30) cc_final: 0.7160 (m-30) REVERT: A 578 ASN cc_start: 0.8018 (m-40) cc_final: 0.7266 (t0) REVERT: A 611 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8456 (mtmm) REVERT: A 648 MET cc_start: 0.6983 (mtm) cc_final: 0.6614 (mtm) REVERT: A 684 ASP cc_start: 0.6941 (t0) cc_final: 0.6458 (p0) REVERT: A 739 VAL cc_start: 0.8277 (m) cc_final: 0.7778 (t) REVERT: B 25 GLU cc_start: 0.7485 (mp0) cc_final: 0.7109 (mp0) REVERT: B 38 MET cc_start: 0.7583 (mmp) cc_final: 0.7345 (mmm) REVERT: B 54 MET cc_start: 0.7993 (ttm) cc_final: 0.7685 (ttm) REVERT: B 109 LEU cc_start: 0.7485 (mm) cc_final: 0.7137 (mt) REVERT: B 110 GLU cc_start: 0.6979 (pp20) cc_final: 0.6605 (pp20) REVERT: B 127 VAL cc_start: 0.8254 (m) cc_final: 0.8044 (p) REVERT: B 137 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7614 (mmtp) REVERT: B 271 LYS cc_start: 0.8332 (mttp) cc_final: 0.7648 (mtmm) REVERT: B 272 GLU cc_start: 0.7680 (tt0) cc_final: 0.6912 (tp30) REVERT: B 280 LYS cc_start: 0.7544 (tttm) cc_final: 0.7170 (mtpt) REVERT: C 29 ILE cc_start: 0.8412 (mt) cc_final: 0.8172 (mm) REVERT: C 54 GLN cc_start: 0.7484 (tt0) cc_final: 0.6802 (tt0) REVERT: C 111 MET cc_start: -0.0595 (ttt) cc_final: -0.1241 (ttt) REVERT: C 116 MET cc_start: 0.7143 (ttm) cc_final: 0.6864 (ttm) REVERT: C 123 MET cc_start: 0.6851 (mtp) cc_final: 0.6324 (mtp) REVERT: C 159 MET cc_start: 0.6675 (mpp) cc_final: 0.6391 (mpp) REVERT: D 86 MET cc_start: 0.6599 (tmm) cc_final: 0.6185 (tmm) REVERT: D 103 ILE cc_start: 0.8366 (mt) cc_final: 0.8015 (tp) REVERT: D 104 MET cc_start: 0.7931 (mmp) cc_final: 0.7627 (mmp) REVERT: D 109 LEU cc_start: 0.8006 (mm) cc_final: 0.7626 (mm) REVERT: D 169 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8284 (ttmt) REVERT: E 82 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7317 (mtmm) REVERT: E 86 GLN cc_start: 0.9041 (mt0) cc_final: 0.8757 (mt0) REVERT: G 12 ASP cc_start: 0.7375 (t0) cc_final: 0.7103 (t0) REVERT: G 43 THR cc_start: 0.8614 (p) cc_final: 0.8358 (t) REVERT: G 132 PRO cc_start: 0.8291 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: H 115 THR cc_start: 0.8792 (m) cc_final: 0.8563 (p) REVERT: H 119 LYS cc_start: 0.7893 (mttm) cc_final: 0.7571 (mttm) REVERT: H 120 LYS cc_start: 0.8412 (tttt) cc_final: 0.8046 (tttt) REVERT: H 127 LYS cc_start: 0.8398 (tttt) cc_final: 0.8176 (tptt) REVERT: I 357 ILE cc_start: 0.2976 (tp) cc_final: 0.2505 (mt) REVERT: I 458 SER cc_start: 0.8325 (m) cc_final: 0.7910 (p) REVERT: I 690 SER cc_start: 0.8203 (m) cc_final: 0.7825 (p) REVERT: I 797 LYS cc_start: 0.7544 (mttt) cc_final: 0.7288 (mttt) REVERT: I 803 THR cc_start: 0.6406 (m) cc_final: 0.5977 (p) REVERT: I 1015 LYS cc_start: 0.8241 (pttm) cc_final: 0.7941 (pttt) REVERT: I 1068 VAL cc_start: 0.7849 (p) cc_final: 0.7518 (t) REVERT: I 1120 ASN cc_start: 0.7218 (t0) cc_final: 0.6865 (t0) REVERT: I 1127 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7765 (mtp180) REVERT: I 1155 LEU cc_start: 0.8515 (mt) cc_final: 0.8283 (mm) outliers start: 1 outliers final: 1 residues processed: 505 average time/residue: 0.1577 time to fit residues: 127.8775 Evaluate side-chains 473 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 218 optimal weight: 5.9990 chunk 196 optimal weight: 0.0670 chunk 231 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN G 63 ASN H 83 ASN ** I 514 HIS ** 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 = 0.3685 r_free = 0.3685 target = 0.130981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113553 restraints weight = 44117.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115131 restraints weight = 28306.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115925 restraints weight = 21693.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116498 restraints weight = 17499.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116623 restraints weight = 16041.668| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23914 Z= 0.164 Angle : 0.640 12.073 32535 Z= 0.330 Chirality : 0.044 0.311 3813 Planarity : 0.004 0.052 4078 Dihedral : 5.597 44.062 3530 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 0.04 % Allowed : 0.80 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2930 helix: 1.58 (0.15), residues: 1208 sheet: 0.82 (0.24), residues: 473 loop : -1.96 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.017 0.002 TYR B 63 PHE 0.021 0.001 PHE A 87 TRP 0.035 0.002 TRP I 137 HIS 0.006 0.001 HIS I 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (23906) covalent geometry : angle 0.63676 / 0.33 (32511) hydrogen bonds : bond 0.05781 / 3.86 ( 1126) hydrogen bonds : angle 4.65959 / 3.24 ( 3306) link_BETA1-4 : bond 0.00297 / 0.15 ( 2) link_BETA1-4 : angle 1.64331 / 0.89 ( 6) link_NAG-ASN : bond 0.00384 / 0.16 ( 6) link_NAG-ASN : angle 2.45715 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 497 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8043 (p) cc_final: 0.7655 (t) REVERT: A 92 ILE cc_start: 0.8800 (tt) cc_final: 0.8351 (mt) REVERT: A 97 ASN cc_start: 0.8299 (m-40) cc_final: 0.8047 (m-40) REVERT: A 169 LEU cc_start: 0.6925 (mt) cc_final: 0.6301 (mt) REVERT: A 210 TRP cc_start: 0.8370 (p-90) cc_final: 0.7668 (p-90) REVERT: A 213 ASP cc_start: 0.7453 (t0) cc_final: 0.6961 (t0) REVERT: A 316 MET cc_start: 0.7830 (mtp) cc_final: 0.7604 (mtp) REVERT: A 317 VAL cc_start: 0.8663 (t) cc_final: 0.8364 (p) REVERT: A 324 TRP cc_start: 0.8152 (p-90) cc_final: 0.7906 (p-90) REVERT: A 406 LEU cc_start: 0.7900 (tp) cc_final: 0.7587 (tt) REVERT: A 457 LYS cc_start: 0.8009 (mmpt) cc_final: 0.7535 (mmpt) REVERT: A 514 THR cc_start: 0.8522 (m) cc_final: 0.8099 (t) REVERT: A 516 GLU cc_start: 0.7160 (tp30) cc_final: 0.6768 (tp30) REVERT: A 569 ASP cc_start: 0.7665 (m-30) cc_final: 0.7384 (m-30) REVERT: A 578 ASN cc_start: 0.7983 (m-40) cc_final: 0.7265 (t0) REVERT: A 611 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8481 (mtmm) REVERT: A 648 MET cc_start: 0.6923 (mtm) cc_final: 0.6570 (mtm) REVERT: A 684 ASP cc_start: 0.6939 (t0) cc_final: 0.6448 (p0) REVERT: A 719 ASP cc_start: 0.6934 (p0) cc_final: 0.6225 (p0) REVERT: B 25 GLU cc_start: 0.7427 (mp0) cc_final: 0.7150 (mp0) REVERT: B 45 LEU cc_start: 0.7958 (tp) cc_final: 0.7734 (tp) REVERT: B 54 MET cc_start: 0.8047 (ttm) cc_final: 0.7665 (ttm) REVERT: B 56 MET cc_start: 0.7918 (ttm) cc_final: 0.7628 (ttm) REVERT: B 127 VAL cc_start: 0.8116 (m) cc_final: 0.7868 (p) REVERT: B 133 LEU cc_start: 0.7999 (tp) cc_final: 0.7664 (tt) REVERT: B 137 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7651 (mmtp) REVERT: B 271 LYS cc_start: 0.8282 (mttp) cc_final: 0.7626 (mtmm) REVERT: B 272 GLU cc_start: 0.7676 (tt0) cc_final: 0.6891 (tp30) REVERT: B 280 LYS cc_start: 0.7299 (tttm) cc_final: 0.6930 (mtmt) REVERT: C 29 ILE cc_start: 0.8388 (mt) cc_final: 0.8141 (mm) REVERT: C 111 MET cc_start: -0.0405 (ttt) cc_final: -0.1139 (ttt) REVERT: C 116 MET cc_start: 0.7066 (ttm) cc_final: 0.6786 (ttm) REVERT: C 123 MET cc_start: 0.6791 (mtp) cc_final: 0.6257 (mtp) REVERT: D 86 MET cc_start: 0.6644 (tmm) cc_final: 0.6007 (tmm) REVERT: D 103 ILE cc_start: 0.8290 (mt) cc_final: 0.7970 (mt) REVERT: D 104 MET cc_start: 0.7880 (mmp) cc_final: 0.7535 (mmp) REVERT: D 109 LEU cc_start: 0.7979 (mm) cc_final: 0.7556 (mm) REVERT: E 82 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7304 (mtmm) REVERT: G 12 ASP cc_start: 0.7322 (t0) cc_final: 0.7063 (t0) REVERT: G 43 THR cc_start: 0.8609 (p) cc_final: 0.8352 (t) REVERT: G 102 LEU cc_start: 0.8605 (tp) cc_final: 0.8401 (tp) REVERT: G 103 ASN cc_start: 0.8129 (m110) cc_final: 0.7856 (m110) REVERT: G 132 PRO cc_start: 0.8295 (Cg_endo) cc_final: 0.7990 (Cg_exo) REVERT: H 119 LYS cc_start: 0.7877 (mttm) cc_final: 0.7520 (mttm) REVERT: H 120 LYS cc_start: 0.8389 (tttt) cc_final: 0.8038 (tttt) REVERT: H 127 LYS cc_start: 0.8417 (tttt) cc_final: 0.8177 (tptt) REVERT: I 458 SER cc_start: 0.8313 (m) cc_final: 0.7882 (p) REVERT: I 467 VAL cc_start: 0.8353 (t) cc_final: 0.8040 (m) REVERT: I 477 PHE cc_start: 0.7963 (t80) cc_final: 0.7451 (t80) REVERT: I 690 SER cc_start: 0.8118 (m) cc_final: 0.7784 (p) REVERT: I 797 LYS cc_start: 0.7440 (mttt) cc_final: 0.7216 (mttt) REVERT: I 803 THR cc_start: 0.6185 (m) cc_final: 0.5682 (p) REVERT: I 826 GLN cc_start: 0.7800 (tp40) cc_final: 0.7343 (tm-30) REVERT: I 828 HIS cc_start: 0.8000 (m-70) cc_final: 0.7650 (m-70) REVERT: I 1015 LYS cc_start: 0.8242 (pttm) cc_final: 0.7941 (ptpp) REVERT: I 1047 GLN cc_start: 0.6001 (mp10) cc_final: 0.5787 (mp10) REVERT: I 1068 VAL cc_start: 0.7681 (p) cc_final: 0.7360 (t) REVERT: I 1120 ASN cc_start: 0.7338 (t0) cc_final: 0.6936 (t0) REVERT: I 1155 LEU cc_start: 0.8549 (mt) cc_final: 0.8263 (mm) outliers start: 1 outliers final: 1 residues processed: 498 average time/residue: 0.1562 time to fit residues: 125.3977 Evaluate side-chains 456 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 59 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 219 optimal weight: 0.4980 chunk 241 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN H 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115354 restraints weight = 44061.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116868 restraints weight = 29270.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117646 restraints weight = 21579.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118257 restraints weight = 17780.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118417 restraints weight = 16588.023| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23914 Z= 0.133 Angle : 0.612 12.341 32535 Z= 0.313 Chirality : 0.043 0.308 3813 Planarity : 0.004 0.061 4078 Dihedral : 5.352 41.432 3530 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.03 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.16), residues: 2930 helix: 1.79 (0.15), residues: 1198 sheet: 0.92 (0.24), residues: 466 loop : -1.91 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 383 TYR 0.016 0.001 TYR B 63 PHE 0.019 0.001 PHE A 87 TRP 0.027 0.001 TRP A 112 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23906) covalent geometry : angle 0.60917 / 0.31 (32511) hydrogen bonds : bond 0.05097 / 3.39 ( 1126) hydrogen bonds : angle 4.48359 / 3.13 ( 3306) link_BETA1-4 : bond 0.00389 / 0.20 ( 2) link_BETA1-4 : angle 1.57881 / 0.85 ( 6) link_NAG-ASN : bond 0.00391 / 0.14 ( 6) link_NAG-ASN : angle 2.33731 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.8767 (tt) cc_final: 0.8308 (mt) REVERT: A 97 ASN cc_start: 0.8085 (m-40) cc_final: 0.7831 (m-40) REVERT: A 125 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6699 (tm-30) REVERT: A 169 LEU cc_start: 0.6924 (mt) cc_final: 0.6278 (mt) REVERT: A 210 TRP cc_start: 0.8349 (p-90) cc_final: 0.7612 (p-90) REVERT: A 213 ASP cc_start: 0.7396 (t0) cc_final: 0.6842 (t0) REVERT: A 316 MET cc_start: 0.7822 (mtp) cc_final: 0.7590 (mtp) REVERT: A 317 VAL cc_start: 0.8673 (t) cc_final: 0.8358 (p) REVERT: A 355 TYR cc_start: 0.7795 (p90) cc_final: 0.7591 (p90) REVERT: A 406 LEU cc_start: 0.7826 (tp) cc_final: 0.7509 (tt) REVERT: A 457 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7764 (mmpt) REVERT: A 481 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7878 (mtpt) REVERT: A 514 THR cc_start: 0.8492 (m) cc_final: 0.8109 (t) REVERT: A 516 GLU cc_start: 0.7150 (tp30) cc_final: 0.6758 (tp30) REVERT: A 569 ASP cc_start: 0.7654 (m-30) cc_final: 0.7399 (m-30) REVERT: A 578 ASN cc_start: 0.7958 (m-40) cc_final: 0.7287 (t0) REVERT: A 611 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8486 (mtmm) REVERT: A 646 GLU cc_start: 0.7272 (pp20) cc_final: 0.6960 (tm-30) REVERT: A 648 MET cc_start: 0.6886 (mtm) cc_final: 0.6514 (mtm) REVERT: A 684 ASP cc_start: 0.6983 (t0) cc_final: 0.6473 (p0) REVERT: A 719 ASP cc_start: 0.7005 (p0) cc_final: 0.6243 (p0) REVERT: A 751 LYS cc_start: 0.8390 (tppt) cc_final: 0.8004 (tptp) REVERT: B 25 GLU cc_start: 0.7426 (mp0) cc_final: 0.7156 (mp0) REVERT: B 43 SER cc_start: 0.8695 (p) cc_final: 0.8471 (p) REVERT: B 54 MET cc_start: 0.7911 (ttm) cc_final: 0.7660 (ttm) REVERT: B 127 VAL cc_start: 0.8069 (m) cc_final: 0.7823 (p) REVERT: B 133 LEU cc_start: 0.7855 (tp) cc_final: 0.7652 (tt) REVERT: B 137 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7676 (mmtp) REVERT: B 271 LYS cc_start: 0.8276 (mttp) cc_final: 0.7732 (mtmm) REVERT: B 272 GLU cc_start: 0.7697 (tt0) cc_final: 0.7016 (tm-30) REVERT: B 273 ILE cc_start: 0.8641 (tp) cc_final: 0.8112 (tp) REVERT: B 280 LYS cc_start: 0.7219 (tttm) cc_final: 0.6911 (mtmt) REVERT: C 7 LEU cc_start: 0.8378 (mm) cc_final: 0.8159 (mm) REVERT: C 29 ILE cc_start: 0.8402 (mt) cc_final: 0.8182 (mm) REVERT: C 111 MET cc_start: -0.0327 (ttt) cc_final: -0.1031 (ttt) REVERT: C 116 MET cc_start: 0.7090 (ttm) cc_final: 0.6823 (ttm) REVERT: C 123 MET cc_start: 0.6784 (mtp) cc_final: 0.6225 (mtp) REVERT: D 86 MET cc_start: 0.6628 (tmm) cc_final: 0.6012 (tmm) REVERT: D 103 ILE cc_start: 0.8345 (mt) cc_final: 0.7941 (mt) REVERT: D 104 MET cc_start: 0.7942 (mmp) cc_final: 0.7575 (mmp) REVERT: E 82 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7305 (mtmm) REVERT: G 12 ASP cc_start: 0.7351 (t0) cc_final: 0.7050 (t0) REVERT: G 43 THR cc_start: 0.8598 (p) cc_final: 0.8362 (t) REVERT: H 119 LYS cc_start: 0.7825 (mttm) cc_final: 0.7495 (mttm) REVERT: H 120 LYS cc_start: 0.8364 (tttt) cc_final: 0.8049 (tttt) REVERT: H 127 LYS cc_start: 0.8408 (tttt) cc_final: 0.8205 (tptt) REVERT: I 458 SER cc_start: 0.8277 (m) cc_final: 0.7885 (p) REVERT: I 467 VAL cc_start: 0.8323 (t) cc_final: 0.7968 (m) REVERT: I 477 PHE cc_start: 0.7994 (t80) cc_final: 0.7482 (t80) REVERT: I 690 SER cc_start: 0.8103 (m) cc_final: 0.7765 (p) REVERT: I 797 LYS cc_start: 0.7466 (mttt) cc_final: 0.7166 (ttmt) REVERT: I 803 THR cc_start: 0.6386 (m) cc_final: 0.5705 (p) REVERT: I 826 GLN cc_start: 0.7758 (tp40) cc_final: 0.7321 (tm-30) REVERT: I 828 HIS cc_start: 0.7982 (m-70) cc_final: 0.7605 (m-70) REVERT: I 1015 LYS cc_start: 0.8208 (pttm) cc_final: 0.7926 (ptpp) REVERT: I 1068 VAL cc_start: 0.7690 (p) cc_final: 0.7337 (t) REVERT: I 1120 ASN cc_start: 0.7414 (t0) cc_final: 0.6962 (t0) REVERT: I 1155 LEU cc_start: 0.8532 (mt) cc_final: 0.8250 (mm) outliers start: 1 outliers final: 1 residues processed: 501 average time/residue: 0.1541 time to fit residues: 124.6632 Evaluate side-chains 457 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 136 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 209 optimal weight: 0.0770 chunk 180 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 214 optimal weight: 0.5980 chunk 250 optimal weight: 0.0270 chunk 160 optimal weight: 0.1980 chunk 274 optimal weight: 5.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 86 GLN G 63 ASN H 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117473 restraints weight = 44197.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118908 restraints weight = 28601.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120251 restraints weight = 20828.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120382 restraints weight = 17134.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120662 restraints weight = 15669.765| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23914 Z= 0.111 Angle : 0.592 12.658 32535 Z= 0.300 Chirality : 0.043 0.303 3813 Planarity : 0.004 0.058 4078 Dihedral : 5.109 42.485 3530 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.36 (0.16), residues: 2930 helix: 1.89 (0.15), residues: 1205 sheet: 0.89 (0.25), residues: 470 loop : -1.78 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.016 0.001 TYR B 63 PHE 0.023 0.001 PHE I1096 TRP 0.027 0.001 TRP I 558 HIS 0.010 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (23906) covalent geometry : angle 0.58966 / 0.30 (32511) hydrogen bonds : bond 0.04370 / 2.88 ( 1126) hydrogen bonds : angle 4.30677 / 3.02 ( 3306) link_BETA1-4 : bond 0.00442 / 0.22 ( 2) link_BETA1-4 : angle 1.59031 / 0.86 ( 6) link_NAG-ASN : bond 0.00487 / 0.23 ( 6) link_NAG-ASN : angle 2.18434 / 1.26 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.8779 (tt) cc_final: 0.8299 (mt) REVERT: A 97 ASN cc_start: 0.8042 (m-40) cc_final: 0.7838 (m-40) REVERT: A 123 LEU cc_start: 0.8409 (mt) cc_final: 0.8148 (mt) REVERT: A 169 LEU cc_start: 0.6903 (mt) cc_final: 0.6331 (mt) REVERT: A 210 TRP cc_start: 0.8317 (p-90) cc_final: 0.7657 (p-90) REVERT: A 213 ASP cc_start: 0.7354 (t0) cc_final: 0.6844 (t0) REVERT: A 317 VAL cc_start: 0.8620 (t) cc_final: 0.8370 (p) REVERT: A 355 TYR cc_start: 0.7705 (p90) cc_final: 0.7505 (p90) REVERT: A 406 LEU cc_start: 0.7788 (tp) cc_final: 0.7454 (tt) REVERT: A 457 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7595 (mmpt) REVERT: A 458 GLU cc_start: 0.7158 (mp0) cc_final: 0.6627 (mp0) REVERT: A 481 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7835 (mttt) REVERT: A 514 THR cc_start: 0.8461 (m) cc_final: 0.8049 (t) REVERT: A 516 GLU cc_start: 0.7195 (tp30) cc_final: 0.6960 (tp30) REVERT: A 519 ILE cc_start: 0.8828 (mt) cc_final: 0.8531 (mm) REVERT: A 550 GLU cc_start: 0.7397 (mp0) cc_final: 0.7152 (mp0) REVERT: A 569 ASP cc_start: 0.7687 (m-30) cc_final: 0.7437 (m-30) REVERT: A 578 ASN cc_start: 0.7967 (m-40) cc_final: 0.7269 (t0) REVERT: A 611 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8480 (mtmm) REVERT: A 648 MET cc_start: 0.6823 (mtm) cc_final: 0.6487 (mtm) REVERT: A 684 ASP cc_start: 0.7044 (t0) cc_final: 0.6496 (p0) REVERT: B 25 GLU cc_start: 0.7377 (mp0) cc_final: 0.7120 (mp0) REVERT: B 36 ILE cc_start: 0.8442 (mm) cc_final: 0.8221 (mt) REVERT: B 54 MET cc_start: 0.7873 (ttm) cc_final: 0.7575 (ttm) REVERT: B 71 GLN cc_start: 0.7093 (tp40) cc_final: 0.6427 (tp40) REVERT: B 108 TYR cc_start: 0.7926 (t80) cc_final: 0.7719 (t80) REVERT: B 133 LEU cc_start: 0.7864 (tp) cc_final: 0.7660 (tt) REVERT: B 137 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7666 (mmtp) REVERT: B 271 LYS cc_start: 0.8281 (mttp) cc_final: 0.7960 (mtmm) REVERT: B 272 GLU cc_start: 0.7613 (tt0) cc_final: 0.7090 (tm-30) REVERT: B 273 ILE cc_start: 0.8602 (tp) cc_final: 0.8001 (tp) REVERT: B 280 LYS cc_start: 0.7052 (tttm) cc_final: 0.6793 (mtmt) REVERT: C 7 LEU cc_start: 0.8264 (mm) cc_final: 0.8017 (mm) REVERT: C 29 ILE cc_start: 0.8332 (mt) cc_final: 0.8102 (mm) REVERT: C 111 MET cc_start: -0.0591 (ttt) cc_final: -0.1232 (ttt) REVERT: C 116 MET cc_start: 0.7095 (ttm) cc_final: 0.6797 (ttm) REVERT: C 123 MET cc_start: 0.6718 (mtp) cc_final: 0.6153 (mtp) REVERT: D 86 MET cc_start: 0.6670 (tmm) cc_final: 0.6053 (tmm) REVERT: D 103 ILE cc_start: 0.8283 (mt) cc_final: 0.7881 (mt) REVERT: D 104 MET cc_start: 0.7884 (mmp) cc_final: 0.7551 (mmp) REVERT: D 109 LEU cc_start: 0.7949 (mm) cc_final: 0.7624 (mm) REVERT: E 82 LYS cc_start: 0.7520 (mtmm) cc_final: 0.7299 (mtmm) REVERT: G 12 ASP cc_start: 0.7317 (t0) cc_final: 0.7039 (t0) REVERT: G 43 THR cc_start: 0.8603 (p) cc_final: 0.8350 (t) REVERT: G 78 SER cc_start: 0.8313 (t) cc_final: 0.7971 (p) REVERT: H 59 MET cc_start: 0.8182 (mtp) cc_final: 0.7962 (mtp) REVERT: H 119 LYS cc_start: 0.7785 (mttm) cc_final: 0.7496 (mttm) REVERT: H 120 LYS cc_start: 0.8328 (tttt) cc_final: 0.8042 (tttt) REVERT: I 451 LEU cc_start: 0.8069 (pt) cc_final: 0.7664 (pp) REVERT: I 458 SER cc_start: 0.8228 (m) cc_final: 0.7818 (p) REVERT: I 467 VAL cc_start: 0.8313 (t) cc_final: 0.8009 (m) REVERT: I 477 PHE cc_start: 0.7948 (t80) cc_final: 0.7374 (t80) REVERT: I 547 PRO cc_start: 0.6699 (Cg_exo) cc_final: 0.6456 (Cg_endo) REVERT: I 690 SER cc_start: 0.8078 (m) cc_final: 0.7713 (p) REVERT: I 711 VAL cc_start: 0.8084 (p) cc_final: 0.7857 (t) REVERT: I 797 LYS cc_start: 0.7383 (mttt) cc_final: 0.7089 (ttmt) REVERT: I 803 THR cc_start: 0.5995 (m) cc_final: 0.5748 (p) REVERT: I 826 GLN cc_start: 0.7669 (tp40) cc_final: 0.7277 (tm-30) REVERT: I 828 HIS cc_start: 0.7971 (m-70) cc_final: 0.7561 (m-70) REVERT: I 995 LEU cc_start: 0.7956 (mt) cc_final: 0.7657 (mm) REVERT: I 1015 LYS cc_start: 0.8182 (pttm) cc_final: 0.7879 (ptpp) REVERT: I 1068 VAL cc_start: 0.7581 (p) cc_final: 0.7162 (t) REVERT: I 1120 ASN cc_start: 0.7443 (t0) cc_final: 0.7019 (t0) REVERT: I 1136 MET cc_start: 0.5066 (mmp) cc_final: 0.3986 (tpp) REVERT: I 1155 LEU cc_start: 0.8486 (mt) cc_final: 0.8217 (mm) outliers start: 1 outliers final: 1 residues processed: 500 average time/residue: 0.1555 time to fit residues: 125.5212 Evaluate side-chains 449 residues out of total 2647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 204 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 235 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 259 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 118 HIS C 161 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 86 GLN H 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115167 restraints weight = 43898.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116326 restraints weight = 29048.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117682 restraints weight = 21271.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117805 restraints weight = 17538.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117956 restraints weight = 15766.241| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23914 Z= 0.126 Angle : 0.613 13.134 32535 Z= 0.308 Chirality : 0.043 0.310 3813 Planarity : 0.004 0.057 4078 Dihedral : 5.071 41.832 3530 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.36 (0.16), residues: 2930 helix: 1.91 (0.15), residues: 1200 sheet: 0.98 (0.25), residues: 466 loop : -1.82 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 255 TYR 0.016 0.001 TYR B 63 PHE 0.015 0.001 PHE I 144 TRP 0.024 0.001 TRP A 112 HIS 0.009 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (23906) covalent geometry : angle 0.61030 / 0.31 (32511) hydrogen bonds : bond 0.04625 / 3.07 ( 1126) hydrogen bonds : angle 4.32334 / 3.02 ( 3306) link_BETA1-4 : bond 0.00373 / 0.19 ( 2) link_BETA1-4 : angle 1.55490 / 0.83 ( 6) link_NAG-ASN : bond 0.00395 / 0.15 ( 6) link_NAG-ASN : angle 2.20338 / 1.27 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.78 seconds wall clock time: 67 minutes 56.56 seconds (4076.56 seconds total)